Merge remote-tracking branch 'origin/master'

Author: nchernia

.gitignore

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

src/org/broad/igv/PreferenceManager.java

@@ -16,17 +16,18 @@
 
 
 import org.apache.log4j.Logger;
+import org.broad.igv.feature.genome.GenomeListItem;
 import org.broad.igv.maf.MAFManager;
 import org.broad.igv.renderer.ColorScaleFactory;
 import org.broad.igv.renderer.ContinuousColorScale;
+import org.broad.igv.sam.AlignmentTrack.ShadeBasesOption;
 import org.broad.igv.track.TrackType;
 import org.broad.igv.ui.AboutDialog;
 import org.broad.igv.ui.UIConstants;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.ui.color.PaletteColorTable;
 import org.broad.igv.ui.util.PropertyManager;
 import org.broad.igv.util.HttpUtils;
-import org.broad.igv.sam.AlignmentTrack.ShadeBasesOption;
 
 import java.awt.*;
 import java.io.File;
@@ -58,13 +59,15 @@ public class PreferenceManager implements PropertyManager {
     public static final String CHART_AUTOSCALE = "CHART.AUTOSCALE";
     public static final String CHART_SHOW_DATA_RANGE = "CHART.SHOW_DATA_RANGE";
 
-    /** Added by Chantal Roth, June 25th 2012 */
+    /**
+     * Added by Chantal Roth, June 25th 2012
+     */
     public static final String IONTORRENT_FLOWDIST_HIDE_FIRST_HP = "IONTORRENT.FLOWDIST_HIDE_FIRST_HP";
     public static final String IONTORRENT_FLOWDIST_BINSIZE = "IONTORRENT.FLOWDIST_BINSIZE";
     public static final String IONTORRENT_FLOWDIST_CHARTTYPE = "IONTORRENT.FLOWDIST_CHARTTYPE";
     public static final String IONTORRENT_SERVER = "IONTORRENT.SERVER";
     public static final String IONTORRENT_RESULTS = "IONTORRENT.RESULTS";
-    
+
     public static final String SAM_ALLELE_THRESHOLD = "SAM.ALLELE_THRESHOLD";
     public static final String SAM_QUALITY_THRESHOLD = "SAM.QUALITY_THRESHOLD";
     public static final String SAM_MAX_INSERT_SIZE_THRESHOLD = "SAM.INSERT_SIZE_THRESHOLD";
@@ -131,6 +134,8 @@ public class PreferenceManager implements PropertyManager {
     final static public String LAST_SESSION_DIRECTORY = "LAST_SESSION_DIRECTORY";
     final static public String DEFAULT_GENOME_KEY = "DEFAULT_GENOME_KEY";
     final static public String LAST_CHROMOSOME_VIEWED_KEY = "LAST_CHROMOSOME_VIEWED_KEY";
+    final static public String HISTORY_DELIMITER = ";";
+    final static public String GENOME_HISTORY_KEY = "GENOME_HISTORY";
 
     final public static String MUTATION_COLOR_TABLE = "MUTATION_COLOR_TABLE";
     final public static String MUTATION_INDEL_COLOR_KEY = "MUTATION_INDEL_COLOR_KEY";
@@ -944,7 +949,7 @@ private void initDefaultValues() {
         defaultValues.put(IONTORRENT_FLOWDIST_CHARTTYPE, "LINE");
         defaultValues.put(IONTORRENT_SERVER, "ioneast.ite");
         defaultValues.put(IONTORRENT_RESULTS, "/results/analysis/output/Home/");
-        
+
         defaultValues.put(CHART_DRAW_TOP_BORDER, "false");
         defaultValues.put(CHART_DRAW_BOTTOM_BORDER, "false");
         defaultValues.put(CHART_COLOR_BORDERS, "true");
@@ -1088,4 +1093,24 @@ public void setPrefsFile(String s) {
         }
     }
 
+    public void saveGenomeHistory(List<GenomeListItem> serverGenomeItemList) {
+        String genomeString = "";
+
+        for (GenomeListItem serverItem : serverGenomeItemList) {
+            genomeString += serverItem.getId() + HISTORY_DELIMITER;
+        }
+
+        genomeString = genomeString.substring(0, genomeString.length() - 1);
+        preferences.put(GENOME_HISTORY_KEY, genomeString);
+    }
+
+    public String[] getGenomeHistory() {
+        String genomeIds = get(GENOME_HISTORY_KEY);
+        if (genomeIds == null) {
+            return new String[0];
+        } else {
+            return genomeIds.split(HISTORY_DELIMITER);
+        }
+
+    }
 }

src/org/broad/igv/batch/CommandExecutor.java

@@ -271,15 +271,15 @@ private String genome(String param1) {
         if (param1 == null) {
             return "ERROR missing genome parameter";
         }
-        String result;
+        String result = "OK";
         String genomeID = param1;
 
-        if (igv.getGenomeIds().contains(genomeID)) {
+        if (igv.getSelectableGenomeIDs().contains(genomeID)) {
             igv.selectGenomeFromList(genomeID);
         } else {
             String genomePath = genomeID;
             if (!ParsingUtils.pathExists(genomePath)) {
-                String workingDirectory = (new File("tmp")).getParent();
+                String workingDirectory = System.getProperty("user.dir", "");
                 genomePath = FileUtils.getAbsolutePath(genomeID, workingDirectory);
             }
             if (ParsingUtils.pathExists(genomePath)) {
@@ -289,11 +289,11 @@ private String genome(String param1) {
                     throw new RuntimeException("Error loading genome: " + genomeID);
                 }
             } else {
-                MessageUtils.showMessage("Warning: Could not locate genome: " + genomeID);
+                result = "ERROR: Could not locate genome: " + genomeID;
+                MessageUtils.showMessage(result);
             }
         }
 
-        result = "OK";
         return result;
     }
 

src/org/broad/igv/data/Interval.java

@@ -18,7 +18,7 @@
  * Interface used to represent data which spans an interval,
  * including the zoom level. If data is different for different
  * zoom levels, merging may not be possible
- *
+ * <p/>
  * User: jacob
  * Date: 2012-Jul-05
  */
@@ -27,35 +27,47 @@ public interface Interval extends Feature {
     /**
      * Determine whether this interval fully contains the specified
      * input interval
+     *
      * @param chr
      * @param start
      * @param end
      * @param zoom
      * @return
      */
-    public boolean contains(String chr, int start, int end, int zoom);
+    boolean contains(String chr, int start, int end, int zoom);
 
     /**
      * Determine whether this interval overlaps the specified
      * interval at all
+     *
      * @param chr
      * @param start
      * @param end
      * @param zoom
      * @return
      */
-    public boolean overlaps(String chr, int start, int end, int zoom);
+    boolean overlaps(String chr, int start, int end, int zoom);
 
 
     /**
      * Merge another interval with this one
+     *
      * @param i
      * @return True if the interval was merged, false
-     * if not. Cannot necessarily merge an interval if there
-     * is no overlap; if the Interval contains data
-     * that data would be missing
+     *         if not. Cannot necessarily merge an interval if there
+     *         is no overlap; if the Interval contains data
+     *         that data would be missing
      */
-    public boolean merge(Interval i);
+    boolean merge(Interval i);
+
+
+    /**
+     * Whether the provided interval can be merged with this one
+     *
+     * @param addingInterval
+     * @return
+     */
+    boolean canMerge(Interval addingInterval);
 
     /**
      * Remove data outside the specified interval.
@@ -69,5 +81,6 @@ public interface Interval extends Feature {
      */
     boolean trimTo(final String chr, final int start, final int end, int zoom);
 
-    public int getZoom();
+    int getZoom();
+
 }

src/org/broad/igv/data/WiggleParser.java

@@ -1,32 +1,25 @@
 /*
- * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
+ * Copyright (c) 2007-2012 The Broad Institute, Inc.
+ * SOFTWARE COPYRIGHT NOTICE
+ * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
  *
  * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
  * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
- *
- * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
- * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
- * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
- * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
- * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
- * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
- * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
- * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
- * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
- * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
  */
 package org.broad.igv.data;
 
-import org.broad.igv.Globals;
-import org.broad.igv.feature.genome.Genome;
-import org.broad.igv.track.TrackType;
-import org.broad.igv.util.collections.FloatArrayList;
-import org.broad.igv.util.collections.IntArrayList;
 import org.apache.log4j.Logger;
+import org.broad.igv.Globals;
 import org.broad.igv.exceptions.ParserException;
+import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.track.TrackProperties;
+import org.broad.igv.track.TrackType;
 import org.broad.igv.util.ParsingUtils;
 import org.broad.igv.util.ResourceLocator;
+import org.broad.igv.util.collections.FloatArrayList;
+import org.broad.igv.util.collections.IntArrayList;
 import org.broad.tribble.readers.AsciiLineReader;
 
 import java.util.HashMap;
@@ -143,7 +136,7 @@ public WiggleDataset parse() {
         try {
             reader = ParsingUtils.openAsciiReader(resourceLocator);
 
-            if (type == type.EXPR) {
+            if (type == Type.EXPR) {
                 reader.readLine(); // Skip header line
             }
 

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

@@ -1,19 +1,12 @@
 /*
- * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
+ * Copyright (c) 2007-2012 The Broad Institute, Inc.
+ * SOFTWARE COPYRIGHT NOTICE
+ * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
  *
  * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
  * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
- *
- * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
- * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
- * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
- * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
- * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
- * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
- * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
- * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
- * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
- * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
  */
 
 /*
@@ -141,16 +134,6 @@ public List<LocusScore> getSegments(String heading, String chr) {
         return (chrSegments == null) ? null : chrSegments.get(chr);
     }
 
-    /**
-     * Method description
-     *
-     * @return
-     */
-    public List<String> getDataHeadings() {
-        return headings;
-    }
-
-
     public List<String> getSampleNames() {
         return headings;
     }
@@ -261,7 +244,7 @@ public void setTrackProperties(TrackProperties props) {
     }
 
     public TrackProperties getTrackProperties() {
-        if(trackProperties == null) {
+        if (trackProperties == null) {
             trackProperties = new TrackProperties();
         }
         return trackProperties;

src/org/broad/igv/dev/db/database.dtd

@@ -0,0 +1,83 @@
+<!--
+  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
+  ~ SOFTWARE COPYRIGHT NOTICE
+  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
+  ~
+  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
+  ~
+  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
+  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+  -->
+
+<!-- Profile describing how to load data from a SQL database-->
+
+<!-- A database element describes a connection to a single database.
+This includes separate path elements (host, path, port).
+
+version
+   Version of the descriptive file, not the database. Used to ensure
+   compatibility with future versions
+name
+    Human-readable name of database
+description
+    Human-readable description
+-->
+<!ELEMENT database (table+)>
+<!ATTLIST database
+      version (alpha) #REQUIRED
+      host CDATA #REQUIRED
+      path CDATA #REQUIRED
+      port CDATA #REQUIRED
+      subprotocol CDATA #REQUIRED
+      username CDATA #REQUIRED
+      name CDATA #REQUIRED
+      description CDATA #IMPLIED>
+
+
+<!--
+A database can have any number of tables within it.
+For each table, we have to specify the location
+of certain columns.
+name
+    Exact name of the table
+description
+    Human-readable description of data
+binColName
+    For efficient lookups, many databases use an r-tree,
+    and store the bin number. See
+    http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
+    for UCSC binning structure. If this column name is provided,
+    we assume such column exists and it uses this binning structure.
+chromoColName
+    Column name which stores chromosome names
+format
+    Table must be in a format which IGV can read, that is,
+    the rows must be in the same order/meaning as one
+    of the file formats IGV can read. "format" is file extension
+    that the table is similar to (e.g. bed, psl, ucscgene).
+    We say "similar" because the startColIndex/endColIndex
+    fields can be used to take a subset of columns
+posStartColName
+    The name of the column which contains the start positions
+    of each feature. Necessary for constructing queries.
+posEndColName
+    Name of the column which contains end positions of each feature.
+startColIndex
+    1-based Column index from which to start reading data. Default 1.
+ endColIndex
+    1-based column index, inclusive, at which to stop reading data.
+    Default 2147483646 (Integer.MAX_VALUE - 1, ie all)
+
+-->
+<!ELEMENT table (#PCDATA)>
+<!ATTLIST table
+      name CDATA #REQUIRED
+      description CDATA #IMPLIED
+      binColName CDATA #IMPLIED
+      chromoColName CDATA #REQUIRED
+      format CDATA #REQUIRED
+      posStartColName CDATA #REQUIRED
+      posEndColName CDATA #REQUIRED
+      startColIndex CDATA "1"
+      endColIndex CDATA "2147483646">
+