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root committed Oct 10, 2011
1 parent 8747d45 commit 0f18bb1
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Showing 17 changed files with 563 additions and 15 deletions.
6 changes: 5 additions & 1 deletion Taxonomy/src/org/simmi/client/Taxonomy.java
Original file line number Diff line number Diff line change
Expand Up @@ -91,10 +91,12 @@ public void onError(Request request, Throwable exception) {
}

public void runStuff( String server, Tree tree ) {
final TreeItem rootitem2 = tree.addItem( "root2" );
final TreeItem rootitem3 = tree.addItem( "root3" );
final TreeItem rootitem4 = tree.addItem( "root4" );
final TreeItem rootitem5 = tree.addItem( "root5" );
final TreeItem rootitem6 = tree.addItem( "root6" );
final TreeItem rootitem12 = tree.addItem( "root12" );
final TreeItem rootitem13 = tree.addItem( "root13" );
final TreeItem rootitem14 = tree.addItem( "root14" );
final TreeItem arciformis = tree.addItem( "arciformis" );
Expand Down Expand Up @@ -150,10 +152,12 @@ public void onSelection(SelectionEvent<TreeItem> event) {

String nodename = selectedtree.getText();
if( ( nodename.contains("root") || nodename.equals("arciformis") || nodename.equals("kawarayensis") ) && selectedtree.getChildCount() == 0 ) {
if( nodename.equals("root3") ) runSpec( selectedtree, "http://"+server+"/3v1.txt" );
if( nodename.equals("root2") ) runSpec( selectedtree, "http://"+server+"/2v1.txt" );
else if( nodename.equals("root3") ) runSpec( selectedtree, "http://"+server+"/3v1.txt" );
else if( nodename.equals("root4") ) runSpec( selectedtree, "http://"+server+"/4v1.txt" );
else if( nodename.equals("root5") ) runSpec( selectedtree, "http://"+server+"/5v1.txt" );
else if( nodename.equals("root6") ) runSpec( selectedtree, "http://"+server+"/6v1.txt" );
else if( nodename.equals("root12") ) runSpec( selectedtree, "http://"+server+"/12v1.txt" );
else if( nodename.equals("root13") ) runSpec( selectedtree, "http://"+server+"/13v1.txt" );
else if( nodename.equals("root14") ) runSpec( selectedtree, "http://"+server+"/14v1.txt" );
else if( nodename.equals("arciformis") ) runSpec( selectedtree, "http://"+server+"/arciformis_v1.txt" );
Expand Down
12 changes: 6 additions & 6 deletions distann/src/org/simmi/GeneSet.java
Original file line number Diff line number Diff line change
Expand Up @@ -2292,7 +2292,7 @@ private static void loci2gene( Reader rd, String outfile, String filtercont, Map
}
fw.write( "total: "+tot+" subtot: "+subtot+"\n" );

FileInputStream gfr = new FileInputStream("/home/horfrae/GbAccList.0918.2011.gz");
FileInputStream gfr = new FileInputStream("/home/sigmar/GbAccList.0918.2011.gz");
GZIPInputStream gzi = new GZIPInputStream( gfr );
BufferedReader gbr = new BufferedReader( new InputStreamReader( gzi ) );
String gline = gbr.readLine();
Expand All @@ -2309,7 +2309,7 @@ private static void loci2gene( Reader rd, String outfile, String filtercont, Map
}
gfr.close();

FileInputStream dfr = new FileInputStream("/home/horfrae/tax/gi_taxid_nucl.dmp.gz");
FileInputStream dfr = new FileInputStream("/home/sigmar/tax/gi_taxid_nucl.dmp.gz");
GZIPInputStream dgzi = new GZIPInputStream( dfr );
BufferedReader dbr = new BufferedReader( new InputStreamReader(dgzi) );
String dstr = dbr.readLine();
Expand All @@ -2324,7 +2324,7 @@ private static void loci2gene( Reader rd, String outfile, String filtercont, Map
dfr.close();

List<String> taxmap = new ArrayList<String>();
FileReader tfr = new FileReader("/home/horfrae/tax/names.dmp");
FileReader tfr = new FileReader("/home/sigmar/tax/names.dmp");
BufferedReader tbr = new BufferedReader( tfr );
String tstr = tbr.readLine();
while( tstr != null ) {
Expand All @@ -2345,7 +2345,7 @@ private static void loci2gene( Reader rd, String outfile, String filtercont, Map
tfr.close();

Map<Integer,Integer> parmap = new HashMap<Integer,Integer>();
FileReader pfr = new FileReader("/home/horfrae/tax/nodes.dmp");
FileReader pfr = new FileReader("/home/sigmar/tax/nodes.dmp");
BufferedReader pbr = new BufferedReader( pfr );
String pstr = pbr.readLine();
while( pstr != null ) {
Expand Down Expand Up @@ -4415,12 +4415,12 @@ public static void main(String[] args) {
//loci2gene( new FileReader("/home/sigmar/flx/islandicus.blastoutcat"), "/home/sigmar/flx/islandicus.txt" );
//loci2gene( new FileReader("/home/sigmar/flx/scoto2127.blastoutcat"), "/home/sigmar/flx/scoto2127.txt" );

Map<String,Integer> freqmap = loadFrequency( new FileReader("/home/horfrae/viggo/4.blastout") );
Map<String,Integer> freqmap = loadFrequency( new FileReader("/home/sigmar/viggo/6.blastout") );
/*for( String val : freqmap.keySet() ) {
int fv = freqmap.get(val);
System.err.println( val + " " + fv );
}*/
loci2gene( new FileReader("/home/horfrae/viggo/4.blastout"), "/home/horfrae/viggo/4v1.txt", null, freqmap );
loci2gene( new FileReader("/home/sigmar/viggo/6.blastout"), "/home/sigmar/viggo/6v1.txt", null, freqmap );

//Map<String,Integer> freqmap = loadFrequency( new FileReader("/home/sigmar/arciformis_repeat.blastout") );
//loci2gene( new FileReader("/home/sigmar/arciformis_repeat.blastout"), "/home/sigmar/arciformis_v1.txt", null, freqmap );
Expand Down
55 changes: 48 additions & 7 deletions navisionexplorer/src/org/simmi/client/Navisionexplorer.java
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@
import com.google.gwt.event.dom.client.DropHandler;
import com.google.gwt.event.logical.shared.ResizeEvent;
import com.google.gwt.event.logical.shared.ResizeHandler;
import com.google.gwt.event.logical.shared.SelectionEvent;
import com.google.gwt.event.logical.shared.SelectionHandler;
import com.google.gwt.event.logical.shared.ValueChangeEvent;
import com.google.gwt.event.logical.shared.ValueChangeHandler;
import com.google.gwt.http.client.Request;
Expand Down Expand Up @@ -152,6 +154,10 @@ public double getKronas() {
return 0;
}

public String getId() {
return id;
}

public String getSvid() {
return svid;
}
Expand Down Expand Up @@ -253,10 +259,11 @@ public void updateVerkTable( List<Verk> vlist ) {
mdata.addRow();

mdata.setValue( r, 0, v.getName() );
mdata.setValue( r, 1, v.getSvid() );
mdata.setValue( r, 1, v.getId() );
mdata.setValue( r, 2, v.getSvid() );
}
jview = DataView.create( jdata );
jtable.draw( jview, joptions );
mview = DataView.create( mdata );
mtable.draw( mview, moptions );
}

public void loadAllJobs( final List<Job> jlist ) {
Expand Down Expand Up @@ -302,7 +309,7 @@ public void onResponseReceived(Request request, Response response) {
vlist.clear();
for( String spl : split ) {
String[] subsplit = spl.split("\t");
if( subsplit.length == 2 ) {
if( subsplit.length == 3 ) {
String name = subsplit[0].trim();
String id = subsplit[1].trim();
String svid = subsplit[2].trim();
Expand Down Expand Up @@ -592,7 +599,7 @@ public void mrepaint( List<? extends Kronas> subverk, String verkname ) {
context.clearRect(0, 0, w, h);

double dtot = Math.round( total*100.0 )/100.0;
context.fillText(verkname + " (" + dtot + " klukkutímar)", 10, 30);
context.fillText(verkname + " (" + dtot + " krónur)", 10, 30);

int c = 0;
double k = 0.0;
Expand Down Expand Up @@ -1087,6 +1094,35 @@ public void onValueChange(ValueChangeEvent<Date> event) {
final List<Verk> vlist = new ArrayList<Verk>();
loadAllVerks( vlist );

final ResizeLayoutPanel mrlp = new ResizeLayoutPanel();
tlp.addSelectionHandler( new SelectionHandler<Integer>() {
@Override
public void onSelection(SelectionEvent<Integer> event) {
Integer sel = event.getSelectedItem();
if( sel != null && table != null && mtable != null ) {
if( sel == 0 ) {
table.draw( view, options );
jtable.draw( jview, joptions );
} else {
//mdata.removeRows(0, mdata.getNumberOfRows());
//updateVerkTable( vlist );
//int w = mrlp.getOffsetWidth();
//int h = mrlp.getOffsetHeight();

int w = m_slp.getOffsetWidth();
int h = m_slp.getOffsetHeight();
int cw = mcanvas.getOffsetWidth();
int sw = m_slp.getSplitterSize();

int ww = w - cw - sw;
mtable.setSize(ww+"px", h+"px");
mtable.draw( mview, moptions );
mtable.setSize(ww+"px", h+"px");
}
}
}
});

canvas = Canvas.createIfSupported();
canvas.setSize("100%", "100%");
/*canvas.addAttachHandler( new AttachEvent.Handler() {
Expand Down Expand Up @@ -1181,6 +1217,9 @@ public void onDrop(DropEvent event) {
}
});

mcanvas = Canvas.createIfSupported();
mcanvas.setSize("100%", "100%");

Runnable onLoadCallback = new Runnable() {
public void run() {
data = DataTable.create();
Expand Down Expand Up @@ -1213,6 +1252,7 @@ public void run() {

mdata = DataTable.create();
mdata.addColumn( ColumnType.STRING, "Verkefni");
mdata.addColumn( ColumnType.STRING, "Verknúmer");
mdata.addColumn( ColumnType.STRING, "Svið");

moptions = Options.create();
Expand All @@ -1223,7 +1263,9 @@ public void run() {
mview = DataView.create( mdata );
mtable = new Table( mview, moptions );

if( vlist.size() > 0 && mdata.getNumberOfRows() < 2 ) updateVerkTable( vlist );
if( vlist.size() > 0 && mdata.getNumberOfRows() < 2 ) {
updateVerkTable( vlist );
}

table.addSelectHandler( new SelectHandler() {
@Override
Expand Down Expand Up @@ -1289,7 +1331,6 @@ public void onResize(ResizeEvent event) {
}
});

ResizeLayoutPanel mrlp = new ResizeLayoutPanel();
mrlp.add( mtable );
mrlp.addResizeHandler( new ResizeHandler() {
@Override
Expand Down
1 change: 0 additions & 1 deletion serifier/src/org/simmi/SerifyApplet.java
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@
import java.awt.event.WindowListener;
import java.io.BufferedReader;
import java.io.ByteArrayOutputStream;
import java.io.Console;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
Expand Down
39 changes: 39 additions & 0 deletions vote/.project
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>vote</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.google.gdt.eclipse.core.webAppProjectValidator</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.google.gwt.eclipse.core.gwtProjectValidator</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.google.appengine.eclipse.core.projectValidator</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>com.google.appengine.eclipse.core.enhancerbuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>com.google.appengine.eclipse.core.gaeNature</nature>
<nature>com.google.gwt.eclipse.core.gwtNature</nature>
</natures>
</projectDescription>
23 changes: 23 additions & 0 deletions vote/src/org/simmi/Vote.gwt.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?>
<module rename-to='vote'>
<!-- Inherit the core Web Toolkit stuff. -->
<inherits name='com.google.gwt.user.User'/>

<!-- Inherit the default GWT style sheet. You can change -->
<!-- the theme of your GWT application by uncommenting -->
<!-- any one of the following lines. -->
<inherits name='com.google.gwt.user.theme.clean.Clean'/>
<!-- <inherits name='com.google.gwt.user.theme.standard.Standard'/> -->
<!-- <inherits name='com.google.gwt.user.theme.chrome.Chrome'/> -->
<!-- <inherits name='com.google.gwt.user.theme.dark.Dark'/> -->

<!-- Other module inherits -->

<!-- Specify the app entry point class. -->
<entry-point class='org.simmi.client.Vote'/>

<!-- Specify the paths for translatable code -->
<source path='client'/>
<source path='shared'/>

</module>
12 changes: 12 additions & 0 deletions vote/src/org/simmi/client/GreetingService.java
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
package org.simmi.client;

import com.google.gwt.user.client.rpc.RemoteService;
import com.google.gwt.user.client.rpc.RemoteServiceRelativePath;

/**
* The client side stub for the RPC service.
*/
@RemoteServiceRelativePath("greet")
public interface GreetingService extends RemoteService {
String greetServer(String name) throws IllegalArgumentException;
}
11 changes: 11 additions & 0 deletions vote/src/org/simmi/client/GreetingServiceAsync.java
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
package org.simmi.client;

import com.google.gwt.user.client.rpc.AsyncCallback;

/**
* The async counterpart of <code>GreetingService</code>.
*/
public interface GreetingServiceAsync {
void greetServer(String input, AsyncCallback<String> callback)
throws IllegalArgumentException;
}
70 changes: 70 additions & 0 deletions vote/src/org/simmi/client/Vote.java
Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
package org.simmi.client;

import com.google.gwt.core.client.EntryPoint;
import com.google.gwt.core.client.GWT;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.http.client.Response;
import com.google.gwt.user.client.ui.Grid;
import com.google.gwt.user.client.ui.Image;
import com.google.gwt.user.client.ui.RootPanel;

/**
* Entry point classes define <code>onModuleLoad()</code>.
*/
public class Vote implements EntryPoint {
/**
* The message displayed to the user when the server cannot be reached or
* returns an error.
*/
private static final String SERVER_ERROR = "An error occurred while "
+ "attempting to contact the server. Please check your network "
+ "connection and try again.";

/**
* Create a remote service proxy to talk to the server-side Greeting service.
*/
private final GreetingServiceAsync greetingService = GWT
.create(GreetingService.class);

/**
* This is the entry point method.
*/
public void onModuleLoad() {
RootPanel rp = RootPanel.get();
final Grid grid = new Grid( 8, 10 );
grid.setSize("100%", "100%");

RequestBuilder rb = new RequestBuilder( RequestBuilder.POST, "/list.txt" );
try {
rb.sendRequest("", new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
String list = response.getText();
String[] lines = list.split("\n");

int i = 0;
for( String name : lines ) {
String[] split = name.split("\t");
if( split.length > 2 ) {
grid.setWidget( i/10, i%10, new Image( split[2] ) );
}

i++;
}
}

@Override
public void onError(Request request, Throwable exception) {

}
});
} catch (RequestException e) {
e.printStackTrace();
}

rp.add( grid );
}
}
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