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jrobinsojrobinso
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Merge remote-tracking branch 'origin/master'
2 parents e6f6e33 + 4349001 commit 03c9ef9

40 files changed

+1277
-356
lines changed

‎.gitignore

+6-1
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@@ -30,4 +30,9 @@ build/
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/web/jnlp.template
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/batik-codec.jar
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/goby-io-igv.jar
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/launcher/dist
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/launcher/dist
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/test/largedata
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#Ignore index files
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*.*.idx
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!isect_res.bed.idx

‎src/org/broad/igv/data/seg/SegmentFileParser.java

+6-13
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@@ -1,19 +1,12 @@
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/*
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* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
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* Copyright (c) 2007-2012 The Broad Institute, Inc.
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* SOFTWARE COPYRIGHT NOTICE
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* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
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*
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* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
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* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
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*
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* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
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* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
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* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
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* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
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* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
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* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
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* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
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* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
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* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
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* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
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*/
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package org.broad.igv.data.seg;
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@@ -189,7 +182,7 @@ public SegmentedAsciiDataSet loadSegments(ResourceLocator locator, Genome genome
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throw new RuntimeException(e);
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}
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} finally {
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if (reader == null) {
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if (reader != null) {
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reader.close();
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}
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}

‎src/org/broad/igv/dev/GenDataParser.java

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@@ -0,0 +1,155 @@
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/*
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* Copyright (c) 2007-2012 The Broad Institute, Inc.
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* SOFTWARE COPYRIGHT NOTICE
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* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
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*
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* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
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* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
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*/
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package org.broad.igv.dev;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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/**
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* User: jacob
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* Date: 2012-Aug-30
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*/
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public class GenDataParser {
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public final byte getByte(ResultSet rs, int index) throws SQLException {
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return rs.getByte(index + 1);
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}
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public final byte getByte(ResultSet rs, String label) throws SQLException {
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return rs.getByte(label);
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}
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public final byte getByte(String[] array, int index) throws NumberFormatException {
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return Byte.valueOf(array[index]);
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}
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public final short getShort(ResultSet rs, int index) throws SQLException {
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return rs.getShort(index + 1);
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}
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public final short getShort(ResultSet rs, String label) throws SQLException {
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return rs.getShort(label);
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}
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public final short getShort(String[] array, int index) throws NumberFormatException {
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return Short.valueOf(array[index]);
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}
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public final int getInt(ResultSet rs, int index) throws SQLException {
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return rs.getInt(index + 1);
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}
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public final int getInt(ResultSet rs, String label) throws SQLException {
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return rs.getInt(label);
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}
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public final int getInt(String[] array, int index) throws NumberFormatException {
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return Integer.valueOf(array[index]);
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}
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public final double getDouble(ResultSet rs, int index) throws SQLException {
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return rs.getDouble(index + 1);
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}
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public final double getDouble(ResultSet rs, String label) throws SQLException {
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return rs.getDouble(label);
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}
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public final double getDouble(String[] array, int index) throws NumberFormatException {
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return Double.valueOf(array[index]);
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}
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public final float getFloat(ResultSet rs, int index) throws SQLException {
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return rs.getFloat(index + 1);
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}
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public final float getFloat(ResultSet rs, String label) throws SQLException {
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return rs.getFloat(label);
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}
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public final float getFloat(String[] array, int index) throws NumberFormatException {
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return Float.valueOf(array[index]);
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}
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public final String getString(ResultSet rs, int index) throws SQLException {
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return rs.getString(index + 1);
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}
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public final String getString(ResultSet rs, String label) throws SQLException {
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return rs.getString(label);
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}
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public final String getString(String[] array, int index) throws NumberFormatException {
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return array[index];
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}
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// public final byte getByte(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getByte(index + 1);
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// }else if(obj instanceof String[]){
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// return Byte.valueOf(((String[]) obj)[index]);
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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// public final short getShort(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getShort(index + 1);
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// }else if(obj instanceof String[]){
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// return Short.valueOf(((String[]) obj)[index]);
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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// public final int getInt(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getInt(index + 1);
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// }else if(obj instanceof String[]){
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// return Integer.valueOf(((String[]) obj)[index]);
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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// public final float getFloat(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getFloat(index + 1);
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// }else if(obj instanceof String[]){
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// return Float.valueOf(((String[]) obj)[index]);
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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// public final double getDouble(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getDouble(index + 1);
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// }else if(obj instanceof String[]){
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// return Double.valueOf(((String[]) obj)[index]);
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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// public final String getString(Object obj, int index) throws SQLException{
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// if(obj instanceof ResultSet){
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// return ((ResultSet) obj).getString(index + 1);
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// }else if(obj instanceof String[]){
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// return ((String[]) obj)[index];
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// }else{
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// throw new IllegalArgumentException("Input must be a ResultSet or String[]");
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// }
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// }
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//
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}

‎src/org/broad/igv/dev/IParser.java

+43
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@@ -0,0 +1,43 @@
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/*
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* Copyright (c) 2007-2012 The Broad Institute, Inc.
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* SOFTWARE COPYRIGHT NOTICE
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* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
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*
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* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
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* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
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*/
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package org.broad.igv.dev;
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import org.broad.igv.exceptions.ParserException;
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/**
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* User: jacob
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* Date: 2012-Aug-30
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*/
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public interface IParser<TContainer, TIndex> {
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byte getByte(TContainer obj, TIndex index) throws ParserException;
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short getShort(TContainer obj, TIndex index) throws ParserException;
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int getInt(TContainer obj, TIndex index) throws ParserException;
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float getFloat(TContainer obj, TIndex index) throws ParserException;
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double getDouble(TContainer obj, TIndex index) throws ParserException;
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String getString(TContainer obj, TIndex index) throws ParserException;
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/**
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* Return the number of data objects contained.
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* For an array, this would be the length
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*
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* @param obj
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* @return
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* @throws ParserException
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*/
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int size(TContainer obj) throws ParserException;
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}

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