X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=8396e6a80d109b87b368ab3296b1a04e3c9aa8d5;hb=071ecbceb65b4207d9ce866ffc0aa31d200d35ef;hp=99cd9365b77333b797e262a25b04903134ea1859;hpb=44f6e9fd1e6df7c78950ef2c778e86add4ec498e;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 99cd936..8396e6a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,18 +1,18 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.gui;
@@ -55,6 +55,7 @@ import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
@@ -69,13 +70,14 @@ import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
import java.awt.Color;
@@ -106,6 +108,7 @@ import java.net.URL;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JButton;
@@ -124,7 +127,7 @@ import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
@@ -156,7 +159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Creates a new AlignFrame object with specific width and height.
- *
+ *
* @param al
* @param width
* @param height
@@ -169,7 +172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
@@ -184,7 +187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Creates a new AlignFrame object with specific width, height and
* sequenceSetId
- *
+ *
* @param al
* @param width
* @param height
@@ -199,7 +202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* new alignment window with hidden columns
- *
+ *
* @param al
* AlignmentI
* @param hiddenColumns
@@ -218,7 +221,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
@@ -235,7 +238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Create alignment frame for al with hiddenColumns, a specific width and
* height, and specific sequenceId
- *
+ *
* @param al
* @param hiddenColumns
* @param width
@@ -264,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Make a new AlignFrame from exisiting alignmentPanels
- *
+ *
* @param ap
* AlignmentPanel
* @param av
@@ -284,7 +287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
void init()
{
- if (viewport.getAlignmentConservationAnnotation()== null)
+ if (viewport.getAlignmentConservationAnnotation() == null)
{
BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
@@ -332,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
- *
+ *
* @param file
* valid filename
* @param format
@@ -349,6 +352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -403,21 +407,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
|| evt.isShiftDown() || evt.isAltDown());
}
break;
-
- //case KeyEvent.VK_A:
- // if (viewport.cursorMode)
- // {
- // alignPanel.seqPanel.insertNucAtCursor(false,"A");
- // //System.out.println("A");
- // }
- // break;
- /*
- case KeyEvent.VK_CLOSE_BRACKET:
- if (viewport.cursorMode)
- {
- System.out.println("closing bracket");
- }
- break;
+
+ // case KeyEvent.VK_A:
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+ // //System.out.println("A");
+ // }
+ // break;
+ /*
+ * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
+ * System.out.println("closing bracket"); } break;
*/
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
@@ -533,6 +533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
@@ -617,6 +618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
// // System.out.println("Discoverer property change.");
@@ -625,6 +627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
System.err
@@ -638,6 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -650,6 +654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
+ @Override
public void run()
{
BuildWebServiceMenu();
@@ -666,11 +671,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
rnahelicesColour.setEnabled(nucleotide);
purinePyrimidineColour.setEnabled(nucleotide);
// Remember AlignFrame always starts as protein
- //if (!nucleotide)
- // {
- // showTr
- // calculateMenu.remove(calculateMenu.getItemCount() - 2);
- // }
+ // if (!nucleotide)
+ // {
+ // showTr
+ // calculateMenu.remove(calculateMenu.getItemCount() - 2);
+ // }
}
/**
@@ -686,7 +691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Need to call this method when tabs are selected for multiple views, or when
* loading from Jalview2XML.java
- *
+ *
* @param av
* AlignViewport
*/
@@ -713,32 +718,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
-
+
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+ rnahelicesColour
+ .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
setShowProductsEnabled();
updateEditMenuBar();
}
-
+ // methods for implementing IProgressIndicator
+ // need to refactor to a reusable stub class
Hashtable progressBars, progressBarHandlers;
/*
* (non-Javadoc)
- *
+ *
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+ @Override
public void setProgressBar(String message, long id)
{
if (progressBars == null)
@@ -786,6 +794,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
validate();
}
+ @Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
{
@@ -803,6 +812,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
@@ -817,9 +827,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
+ @Override
public boolean operationInProgress()
{
if (progressBars != null && progressBars.size() > 0)
@@ -842,20 +853,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
}
+ @Override
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+ @Override
public void addFromFile_actionPerformed(ActionEvent e)
{
Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
{
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
if (currentFileFormat.equals("Jalview"))
@@ -864,7 +880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
{
@@ -901,6 +917,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final FeatureSettings nfs = newframe.featureSettings;
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
nfs.frame.setBounds(fspos);
@@ -914,16 +931,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void addFromText_actionPerformed(ActionEvent e)
{
Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
}
+ @Override
public void addFromURL_actionPerformed(ActionEvent e)
{
Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null
@@ -941,10 +961,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAs_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1036,10 +1057,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(format,
- (Alignment) viewport.getAlignment(), // class cast exceptions will
+ String output = f.formatSequences(
+ format,
+ viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
- omitHidden, f.getCacheSuffixDefault(format), viewport.getColumnSelection());
+ omitHidden, f.getCacheSuffixDefault(format),
+ viewport.getColumnSelection());
if (output == null)
{
@@ -1091,10 +1114,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void outputText_actionPerformed(ActionEvent e)
{
String[] omitHidden = null;
@@ -1122,7 +1146,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
try
{
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.getAlignment(), omitHidden, viewport.getColumnSelection()));
+ viewport.getAlignment(), omitHidden,
+ viewport.getColumnSelection()));
Desktop.addInternalFrame(cap,
"Alignment output - " + e.getActionCommand(), 600, 500);
} catch (OutOfMemoryError oom)
@@ -1135,10 +1160,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
new HTMLOutput(alignPanel,
@@ -1153,10 +1179,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1164,15 +1191,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createEPS(File f)
{
alignPanel.makeEPS(f);
}
+ @Override
public void pageSetup_actionPerformed(ActionEvent e)
{
PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1181,10 +1210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
@@ -1192,21 +1222,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
thread.start();
}
+ @Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter().exportFeatures(alignPanel);
}
+ @Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(
- alignPanel,
+ new AnnotationExporter().exportAnnotations(alignPanel,
viewport.showAnnotation ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport.getAlignment()
- .getGroups(),
- ((Alignment) viewport.getAlignment()).alignmentProperties);
+ .getAlignmentAnnotation() : null, viewport
+ .getAlignment().getGroups(), ((Alignment) viewport
+ .getAlignment()).alignmentProperties);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
@@ -1230,9 +1262,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Close the current view or all views in the alignment frame. If the frame
* only contains one view then the alignment will be removed from memory.
- *
+ *
* @param closeAllTabs
*/
+ @Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (alignPanels != null && alignPanels.size() < 2)
@@ -1275,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* close alignPanel2 and shuffle tabs appropriately.
- *
+ *
* @param alignPanel2
*/
public void closeView(AlignmentPanel alignPanel2)
@@ -1343,14 +1376,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.redoList.clear();
updateEditMenuBar();
viewport.updateHiddenColumns();
-// viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
-// && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
-// .getHiddenColumns().size() > 0);
+ // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
}
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
@@ -1375,10 +1409,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
@@ -1392,25 +1427,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- if (originalSource!=viewport)
+ if (originalSource != viewport)
{
- Cache.log.warn("Implementation worry: mismatch of viewport origin for undo");
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
-// originalSource.hasHiddenColumns = (viewport.getColumnSelection() != null
-// && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
-// .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.redoList.size() < 1)
@@ -1428,16 +1467,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- if (originalSource!=viewport)
+ if (originalSource != viewport)
{
- Cache.log.warn("Implementation worry: mismatch of viewport origin for redo");
+ Cache.log
+ .warn("Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
- //originalSource.hasHiddenColumns = (viewport.getColumnSelection() != null
- // && viewport.getColumnSelection().getHiddenColumns() != null && viewport.getColumnSelection()
- // .getHiddenColumns().size() > 0);
- originalSource.firePropertyChange("alignment", null,
- originalSource.getAlignment().getSequences());
+ // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+ // null
+ // && viewport.getColumnSelection().getHiddenColumns() != null &&
+ // viewport.getColumnSelection()
+ // .getHiddenColumns().size() > 0);
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
}
}
@@ -1485,7 +1527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param up
* DOCUMENT ME!
*/
@@ -1497,66 +1539,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
return;
}
-
- if (up)
- {
- for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);
-
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
-
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.getAlignment().getSequences().setElementAt(temp, i);
- viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
- }
- }
-
+ viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List sg = new Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.getAlignment()
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
- .getHeight())
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
{
sg = viewport.getSelectionGroup().getSequences(
viewport.getHiddenRepSequences());
@@ -1575,9 +1572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
@@ -1632,10 +1627,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1700,10 +1696,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1711,10 +1708,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1722,7 +1720,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Paste contents of Jalview clipboard
- *
+ *
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
*/
@@ -1783,6 +1781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups=new ArrayList();
+ int fgroup=-1;
if (newAlignment)
{
@@ -1850,6 +1850,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
newDs.clear(); // tidy up
}
+ if (alignment.getAlignmentAnnotation()!=null)
+ {
+ for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+ {
+ if (alan.graphGroup>fgroup)
+ {
+ fgroup=alan.graphGroup;
+ }
+ }
+ }
if (pastedal.getAlignmentAnnotation() != null)
{
// Add any annotation attached to alignment.
@@ -1860,6 +1870,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
{
AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+ if (newann.graphGroup>-1)
+ {
+ if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ {
+ for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ }
+
newann.padAnnotation(alwidth);
alignment.addAnnotation(newann);
}
@@ -1879,11 +1902,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (sequences[i].getAnnotation() != null)
{
+ AlignmentAnnotation newann;
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
- sequences[i].getAnnotation()[a].adjustForAlignment();
- sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+ newann=sequences[i].getAnnotation()[a];
+ newann.adjustForAlignment();
+ newann.padAnnotation(alwidth);
+ if (newann.graphGroup>-1)
+ {
+ if (newann.graphGroup>-1)
+ {
+ if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ {
+ for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ {
+ newGraphGroups.add(q, null);
+ }
+ newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ }
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ }
+ }
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
// was
// duplicated
@@ -1923,6 +1963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newann.padAnnotation(avwidth);
alview[avnum].addAnnotation(newann); // annotation was
// duplicated earlier
+ // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
@@ -1932,6 +1973,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
+ if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector)alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }} else { alignPanel.validateAnnotationDimensions(false);}
}
else
@@ -1991,10 +2036,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void cut_actionPerformed(ActionEvent e)
{
copy_actionPerformed(null);
@@ -2003,10 +2049,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -2063,10 +2110,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
viewport.getAlignment().deleteAllGroups();
@@ -2079,10 +2127,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = new SequenceGroup();
@@ -2101,10 +2150,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.cursorMode)
@@ -2124,10 +2174,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2149,6 +2200,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
@@ -2158,10 +2210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2169,10 +2222,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2226,12 +2280,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(trimRegion);
- Vector groups = viewport.getAlignment().getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg :viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.get(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
@@ -2246,10 +2296,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2268,7 +2319,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
addHistoryItem(removeGapCols);
@@ -2292,10 +2344,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
int start = 0, end = viewport.getAlignment().getWidth() - 1;
@@ -2330,10 +2383,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
viewport.setPadGaps(padGapsMenuitem.isSelected());
@@ -2353,22 +2407,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
new Finder();
}
+ @Override
public void newView_actionPerformed(ActionEvent e)
{
newView(true);
}
/**
- *
+ *
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
@@ -2379,7 +2435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @return new alignment panel, already displayed.
@@ -2390,7 +2446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @param copyAnnotation
@@ -2472,11 +2528,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return newap;
}
+ @Override
public void expandViews_actionPerformed(ActionEvent e)
{
Desktop.instance.explodeViews(this);
}
+ @Override
public void gatherViews_actionPerformed(ActionEvent e)
{
Desktop.instance.gatherViews(this);
@@ -2484,10 +2542,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
new FontChooser(alignPanel);
@@ -2495,10 +2554,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2508,12 +2568,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.rightAlignIds = idRightAlign.isSelected();
alignPanel.paintAlignment(true);
}
+ @Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
@@ -2522,9 +2584,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+ @Override
protected void followHighlight_actionPerformed()
{
if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2536,10 +2599,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2548,10 +2612,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2561,17 +2626,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
}
+ @Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+ @Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
repaint();
}
+ @Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
viewport.hideAllSelectedSeqs();
@@ -2580,7 +2648,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* called by key handler and the hide all/show all menu items
- *
+ *
* @param toggleSeqs
* @param toggleCols
*/
@@ -2594,8 +2662,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// Hide everything by the current selection - this is a hack - we do the
// invert and then hide
// first check that there will be visible columns after the invert.
- if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
- .getSelected().size() > 0)
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
.getEndRes()))
{
@@ -2623,7 +2692,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
hideSelSequences_actionPerformed(null);
hide = true;
}
- else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
{
showAllSeqs_actionPerformed(null);
}
@@ -2648,11 +2718,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+ @Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
@@ -2660,11 +2731,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
SequenceGroup sg = viewport.getSelectionGroup();
@@ -2676,11 +2748,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
@@ -2688,12 +2761,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ @Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
+ @Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2702,10 +2777,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2714,10 +2790,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2726,10 +2803,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2738,10 +2816,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2750,10 +2829,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2762,10 +2842,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2774,6 +2855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2792,10 +2874,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2808,10 +2891,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2831,16 +2915,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
}
+ @Override
public void alignmentProperties()
{
JEditorPane editPane = new JEditorPane("text/html", "");
@@ -2857,10 +2943,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
if (alignPanel.overviewPanel != null)
@@ -2877,6 +2964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -2887,6 +2975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2894,10 +2983,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2905,23 +2995,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(
- viewport.getAlignment().getSequences(),
- viewport.getAlignment().getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void zappoColour_actionPerformed(ActionEvent e)
{
changeColour(new ZappoColourScheme());
@@ -2929,10 +3019,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void taylorColour_actionPerformed(ActionEvent e)
{
changeColour(new TaylorColourScheme());
@@ -2940,10 +3031,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void hydrophobicityColour_actionPerformed(ActionEvent e)
{
changeColour(new HydrophobicColourScheme());
@@ -2951,10 +3043,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void helixColour_actionPerformed(ActionEvent e)
{
changeColour(new HelixColourScheme());
@@ -2962,10 +3055,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void strandColour_actionPerformed(ActionEvent e)
{
changeColour(new StrandColourScheme());
@@ -2973,10 +3067,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void turnColour_actionPerformed(ActionEvent e)
{
changeColour(new TurnColourScheme());
@@ -2984,10 +3079,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void buriedColour_actionPerformed(ActionEvent e)
{
changeColour(new BuriedColourScheme());
@@ -2995,30 +3091,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void nucleotideColour_actionPerformed(ActionEvent e)
{
changeColour(new NucleotideColourScheme());
}
+ @Override
public void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
changeColour(new PurinePyrimidineColourScheme());
}
+
/*
- public void covariationColour_actionPerformed(ActionEvent e)
- {
- changeColour(new CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation()[0]));
- }
- */
+ * public void covariationColour_actionPerformed(ActionEvent e) {
+ * changeColour(new
+ * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+ * ()[0])); }
+ */
+ @Override
public void annotationColour_actionPerformed(ActionEvent e)
{
new AnnotationColourChooser(viewport, alignPanel);
}
-
+
+ @Override
public void rnahelicesColour_actionPerformed(ActionEvent e)
{
new RNAHelicesColourChooser(viewport, alignPanel);
@@ -3026,10 +3127,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -3037,12 +3139,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
*/
public void changeColour(ColourSchemeI cs)
{
+ // TODO: compare with applet and pull up to model method
int threshold = 0;
if (cs != null)
@@ -3089,12 +3192,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getColourAppliesToAllGroups())
{
- Vector groups = viewport.getAlignment().getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ {
if (cs == null)
{
sg.cs = null;
@@ -3103,9 +3204,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.getHiddenRepSequences()),
- sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg, viewport
+ .getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
@@ -3115,7 +3215,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
@@ -3139,9 +3239,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3, sg.getSequences(viewport
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
c.verdict(false, viewport.getConsPercGaps());
sg.cs.setConservation(c);
@@ -3163,10 +3263,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyPID_actionPerformed(ActionEvent e)
{
if (viewport.getAbovePIDThreshold()
@@ -3180,14 +3281,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme()!= null)
+ && viewport.getGlobalColourScheme() != null)
{
SliderPanel.setConservationSlider(alignPanel,
viewport.getGlobalColourScheme(), "Background");
@@ -3197,10 +3299,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3215,10 +3318,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void abovePIDThreshold_actionPerformed(ActionEvent e)
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3233,10 +3337,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void userDefinedColour_actionPerformed(ActionEvent e)
{
if (e.getActionCommand().equals("User Defined..."))
@@ -3278,6 +3383,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
radioItem.setName("USER_DEFINED");
radioItem.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
if (evt.isControlDown()
@@ -3300,6 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3311,6 +3418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3325,10 +3433,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PIDColour_actionPerformed(ActionEvent e)
{
changeColour(new PIDColourScheme());
@@ -3336,10 +3445,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
changeColour(new Blosum62ColourScheme());
@@ -3347,10 +3457,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3363,24 +3474,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
alignPanel.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3392,10 +3506,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3408,10 +3523,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
new RedundancyPanel(alignPanel, this);
@@ -3419,10 +3535,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
if ((viewport.getSelectionGroup() == null)
@@ -3442,10 +3559,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void PCAMenuItem_actionPerformed(ActionEvent e)
{
if (((viewport.getSelectionGroup() != null)
@@ -3465,6 +3583,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3474,6 +3593,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getAlignment().getSequences());
}
}
+
+ @Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
@@ -3484,12 +3605,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.followSelection = listenToViewSelections.isSelected();
}
+
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3497,10 +3620,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
@@ -3508,10 +3632,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -3519,10 +3644,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
@@ -3530,7 +3656,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param type
* DOCUMENT ME!
* @param pwType
@@ -3554,13 +3680,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return;
}
- int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize())
+ for (SequenceI _s:sg.getSequences())
{
- if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+ if (_s.getLength() < sg
.getEndRes())
{
JOptionPane
@@ -3618,7 +3743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param title
* DOCUMENT ME!
* @param order
@@ -3631,6 +3756,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3639,8 +3765,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// pointers
AlignmentSorter.sortBy(viewport.getAlignment(), order);
- addHistoryItem(new OrderCommand(order.getName(), oldOrder,
- viewport.getAlignment()));
+ addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
+ .getAlignment()));
alignPanel.paintAlignment(true);
}
@@ -3649,7 +3775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Add a new sort by annotation score menu item
- *
+ *
* @param sort
* the menu to add the option to
* @param scoreLabel
@@ -3663,6 +3789,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3685,8 +3812,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* search the alignment and rebuild the sort by annotation score submenu the
* last alignment annotation vector hash is stored to minimize cost of
* rebuilding in subsequence calls.
- *
+ *
*/
+ @Override
public void buildSortByAnnotationScoresMenu()
{
if (viewport.getAlignment().getAlignmentAnnotation() == null)
@@ -3700,10 +3828,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// almost certainly a quicker way to do this - but we keep it simple
Hashtable scoreSorts = new Hashtable();
AlignmentAnnotation aann[];
- Enumeration sq = viewport.getAlignment().getSequences().elements();
- while (sq.hasMoreElements())
+ for (SequenceI sqa:viewport.getAlignment().getSequences())
{
- aann = ((SequenceI) sq.nextElement()).getAnnotation();
+ aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
{
if (aann[i].hasScore() && aann[i].sequenceRef != null)
@@ -3732,12 +3859,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
+ *
* @param treePanel
* Displayed tree window.
* @param title
* SortBy menu item title.
*/
+ @Override
public void buildTreeMenu()
{
sortByTreeMenu.removeAll();
@@ -3771,11 +3899,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
tp.sortByTree_actionPerformed(null);
addHistoryItem(tp.sortAlignmentIn(alignPanel));
-
+
}
});
@@ -3799,7 +3928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
- *
+ *
*/
public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
{
@@ -3814,7 +3943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
* SequenceI[sz = seqs.getSize(false)];
- *
+ *
* for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
* seqs.getSequenceAt(i); }
*/
@@ -3824,9 +3953,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
/*
* Vector seqs = viewport.getAlignment().getSequences();
- *
+ *
* if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
- *
+ *
* for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
* seqs.elementAt(i); } }
*/
@@ -3872,10 +4001,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
@@ -3911,6 +4041,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
@@ -3931,7 +4067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Add a treeviewer for the tree extracted from a newick file object to the
* current alignment view
- *
+ *
* @param nf
* the tree
* @param title
@@ -3982,7 +4118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
@@ -4001,6 +4137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
buildingMenu = true;
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
@@ -4017,20 +4154,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// TODO: group services by location as well as function and/or
// introduce
// object broker mechanism.
- final Vector wsmenu = new Vector();
+ final Vector wsmenu = new Vector();
final IProgressIndicator af = me;
final JMenu msawsmenu = new JMenu("Alignment");
final JMenu secstrmenu = new JMenu(
"Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu(
- "Sequence Database Search");
- final JMenu analymenu = new JMenu(
- "Analysis");
- // JAL-940 - only show secondary structure prediction services from the legacy server
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ final JMenu analymenu = new JMenu("Analysis");
+ final JMenu dismenu = new JMenu("Protein Disorder");
+ // JAL-940 - only show secondary structure prediction services from
+ // the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null
- && (Discoverer.services.size() > 0))
+ // &&
+ Discoverer.services != null && (Discoverer.services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
@@ -4038,7 +4174,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
Vector secstrpr = (Vector) Discoverer.services
.get("SecStrPred");
- Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch");
+ Vector seqsrch = null; // (Vector)
+ // Discoverer.services.get("SeqSearch");
// TODO: move GUI generation code onto service implementation - so a
// client instance attaches itself to the GUI with method call like
// jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
@@ -4082,27 +4219,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
- // TODO: move into separate menu builder class.
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- jws2servs.attachWSMenuEntry(msawsmenu, me);
- }
- }
- }
- // Add all submenus in the order they should appear on the web services menu
+ // Add all submenus in the order they should appear on the web
+ // services menu
wsmenu.add(msawsmenu);
wsmenu.add(secstrmenu);
+ wsmenu.add(dismenu);
wsmenu.add(analymenu);
+ // final ArrayList submens=new ArrayList();
+ // submens.add(msawsmenu);
+ // submens.add(secstrmenu);
+ // submens.add(dismenu);
+ // submens.add(analymenu);
+
// No search services yet
// wsmenu.add(seqsrchmenu);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
try
@@ -4113,17 +4247,49 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- webService.add((JMenu) wsmenu.get(i));
+ webService.add(wsmenu.get(i));
}
}
else
{
webService.add(me.webServiceNoServices);
}
+ // TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
+ {
+ if (jws2servs.hasServices())
+ {
+ jws2servs.attachWSMenuEntry(webService, me);
+ }
+ if (jws2servs.isRunning())
+ {
+ JMenuItem tm = new JMenuItem(
+ "Still discovering JABA Services");
+ tm.setEnabled(false);
+ webService.add(tm);
+ }
+ }
+ }
+
build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
+ for (JMenu item : wsmenu)
+ {
+ if (item.getItemCount() == 0)
+ {
+ item.setEnabled(false);
+ }
+ else
+ {
+ item.setEnabled(true);
+ }
+ }
} catch (Exception e)
{
+ Cache.log.debug("Exception during web service menu building process.",e);
}
;
}
@@ -4139,10 +4305,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
-
/**
* construct any groupURL type service menu entries.
- *
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
@@ -4152,20 +4317,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
- *
+ *
* @Override public void actionPerformed(ActionEvent e) {
- * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.getAlignment(),
+ * jalview.datamodel.AlignmentView
+ * .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
- *
+ *
* }); webService.add(testAlView);
*/
// TODO: refactor to RestClient discoverer and merge menu entries for
// rest-style services with other types of analysis/calculation service
// SHmmr test client - still being implemented.
// DEBUG - alignmentView
-
- for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
- client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
+
+ for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+ .getRestClients())
+ {
+ client.attachWSMenuEntry(
+ JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+ this);
}
if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
@@ -4179,12 +4349,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
* chooser = new JalviewFileChooser(jalview.bin.Cache.
* getProperty("LAST_DIRECTORY"));
- *
+ *
* chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
* to Vamsas file"); chooser.setToolTipText("Export");
- *
+ *
* int value = chooser.showSaveDialog(this);
- *
+ *
* if (value == JalviewFileChooser.APPROVE_OPTION) {
* jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
* //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
@@ -4192,7 +4362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
@@ -4212,7 +4382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* search selection for sequence xRef products and build the show products
* menu.
- *
+ *
* @param selection
* @param dataset
* @return true if showProducts menu should be enabled.
@@ -4242,6 +4412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
xtype.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: new thread for this call with vis-delay
@@ -4275,6 +4446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
@@ -4358,6 +4530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showProducts_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4391,6 +4564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showTranslation_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4429,7 +4603,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Try to load a features file onto the alignment.
- *
+ *
* @param file
* contents or path to retrieve file
* @param type
@@ -4441,11 +4615,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(file, type)
- .parse(viewport.getAlignment().getDataset(),
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- false, jalview.bin.Cache.getDefault(
- "RELAXEDSEQIDMATCHING", false));
+ featuresFile = new FeaturesFile(file, type).parse(viewport
+ .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, false,
+ jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
@@ -4470,22 +4643,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return featuresFile;
}
+ @Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+ @Override
public void dragExit(DropTargetEvent evt)
{
}
+ @Override
public void dragOver(DropTargetDragEvent evt)
{
}
+ @Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
+ @Override
public void drop(DropTargetDropEvent evt)
{
Transferable t = evt.getTransferable();
@@ -4571,7 +4749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int l = 0, c = pdbfn.indexOf(".");
while (mtch == null && c != -1)
{
- do
+ do
{
l = c;
} while ((c = pdbfn.indexOf(".", l)) > l);
@@ -4624,18 +4802,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// try and associate
// TODO: may want to set a standard ID naming formalism for
// associating PDB files which have no IDs.
- for (SequenceI toassoc: (SequenceI[])fm[2]) {
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0], (String) fm[1],
- toassoc, false);
- if (pe != null)
+ for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- System.err
- .println("Associated file : " + ((String) fm[0])
- + " with "
- + toassoc.getDisplayId(true));
- assocfiles++;
- }
+ PDBEntry pe = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq((String) fm[0],
+ (String) fm[1], toassoc, false);
+ if (pe != null)
+ {
+ System.err.println("Associated file : "
+ + ((String) fm[0]) + " with "
+ + toassoc.getDisplayId(true));
+ assocfiles++;
+ }
}
alignPanel.paintAlignment(true);
}
@@ -4674,7 +4852,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* it's and Annotation file, then a JNet file, and finally a features file. If
* all are false then the user may have dropped an alignment file onto this
* AlignFrame.
- *
+ *
* @param file
* either a filename or a URL string.
*/
@@ -4697,54 +4875,92 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (!isAnnotation)
{
- // try to see if its a JNet 'concise' style annotation file *before* we
- // try to parse it as a features file
- if (format == null)
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
{
- format = new IdentifyFile().Identify(file, protocol);
- }
- if (format.equalsIgnoreCase("JnetFile"))
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar
+ .setText("Successfully pasted T-Coffee scores to alignment.");
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching process didn't work
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
+ "Problem reading T-COFFEE score file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
- protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(), 0, false);
- isAnnotation = true;
+ Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ tcf = null;
}
- else
+ if (tcf == null)
{
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id try
- * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
- * File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
- * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
- * attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
- * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
- * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
- * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
- * System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
// try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (format == null)
+ {
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ isAnnotation = true;
}
else
{
- alignPanel.paintAlignment(true);
+ /*
+ * if (format.equalsIgnoreCase("PDB")) {
+ *
+ * String pdbfn = ""; // try to match up filename with sequence id
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
}
@@ -4760,8 +4976,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
ex.printStackTrace();
}
+ catch (OutOfMemoryError oom)
+ {
+ try {
+ System.gc();
+ } catch (Exception x){};
+ new OOMWarning("loading data "+(protocol!=null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." : "using "+protocol+" from "+file) : ".")+(format!=null ? "(parsing as '"+format+"' file)" :""), oom, Desktop.desktop);
+ }
}
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
@@ -4772,6 +4996,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
@@ -4796,6 +5021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Open the dialog for regex description parsing.
*/
+ @Override
protected void extractScores_actionPerformed(ActionEvent e)
{
ParseProperties pp = new jalview.analysis.ParseProperties(
@@ -4813,11 +5039,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+ @Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4825,10 +5052,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+ @Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4837,7 +5065,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* find the viewport amongst the tabs in this alignment frame and close that
* tab
- *
+ *
* @param av
*/
public boolean closeView(AlignViewport av)
@@ -4878,11 +5106,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4898,43 +5128,61 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
final AlignFrame me = this;
new Thread(new Runnable()
{
+ @Override
public void run()
{
final jalview.ws.SequenceFetcher sf = SequenceFetcher
.getSequenceFetcherSingleton(me);
- final String[] otherdb = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
-
+ String[] dbclasses = sf.getOrderedSupportedSources();
+ // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ // jalview.util.QuickSort.sort(otherdb, otherdb);
+ List otherdb;
JMenu dfetch = new JMenu();
- JMenuItem fetchr;
- rfetch.add(dfetch);
- int comp = 0, mcomp = 15;
+ JMenu ifetch = new JMenu();
+ JMenuItem fetchr = null;
+ int comp = 0, icomp = 0, mcomp = 15;
String mname = null;
- if (otherdb != null && otherdb.length > 0)
+ int dbi = 0;
+ for (String dbclass : dbclasses)
{
- for (int i = 0; i < otherdb.length; i++)
+ otherdb = sf.getSourceProxy(dbclass);
+ // add a single entry for this class, or submenu allowing 'fetch
+ // all' or pick one
+ if (otherdb == null || otherdb.size() < 1)
{
- String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
- if (mname == null)
- {
- mname = "from '" + dbname + "'";
- }
- fetchr = new JMenuItem(otherdb[i]);
- final String[] dassource = new String[]
- { otherdb[i] };
+ continue;
+ }
+ // List dbs=otherdb;
+ // otherdb=new ArrayList();
+ // for (DbSourceProxy db:dbs)
+ // {
+ // if (!db.isA(DBRefSource.ALIGNMENTDB)
+ // }
+ if (mname == null)
+ {
+ mname = "From " + dbclass;
+ }
+ if (otherdb.size() == 1)
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4946,17 +5194,112 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
});
- fetchr.setToolTipText("Retrieve from " + dbname);
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + src.getDbName()) + "");
dfetch.add(fetchr);
- if (comp++ == mcomp || i == (otherdb.length - 1))
+ comp++;
+ }
+ else
+ {
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
+ // fetch all entry
+ DbSourceProxy src = otherdb.get(0);
+ fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
+ + "'");
+ fetchr.addActionListener(new ActionListener()
{
- dfetch.setText(mname + " to '" + dbname + "'");
- rfetch.add(dfetch);
- dfetch = new JMenu();
- mname = null;
- comp = 0;
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassource)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+ });
+
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from all "
+ + otherdb.size() + " sources in "
+ + src.getDbSource() + "
First is :"
+ + src.getDbName()) + "");
+ dfetch.add(fetchr);
+ comp++;
+ // and then build the rest of the individual menus
+ ifetch = new JMenu("Sources from " + src.getDbSource());
+ icomp = 0;
+ String imname = null;
+ int i = 0;
+ for (DbSourceProxy sproxy : otherdb)
+ {
+ String dbname = sproxy.getDbName();
+ String sname = dbname.length() > 5 ? dbname.substring(0,
+ 5) + "..." : dbname;
+ String msname = dbname.length() > 10 ? dbname.substring(
+ 0, 10) + "..." : dbname;
+ if (imname == null)
+ {
+ imname = "from '" + sname + "'";
+ }
+ fetchr = new JMenuItem(msname);
+ final DbSourceProxy[] dassrc =
+ { sproxy };
+ fetchr.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ new jalview.ws.DBRefFetcher(alignPanel.av
+ .getSequenceSelection(),
+ alignPanel.alignFrame, dassrc)
+ .fetchDBRefs(false);
+ }
+ }).start();
+ }
+
+ });
+ fetchr.setToolTipText(""
+ + JvSwingUtils.wrapTooltip("Retrieve from "
+ + dbname) + "");
+ ifetch.add(fetchr);
+ ++i;
+ if (++icomp >= mcomp || i == (otherdb.size()))
+ {
+ ifetch.setText(imname + " to '" + sname + "'");
+ dfetch.add(ifetch);
+ ifetch = new JMenu();
+ imname = null;
+ icomp = 0;
+ comp++;
+ }
}
}
+ ++dbi;
+ if (comp >= mcomp || dbi >= (dbclasses.length))
+ {
+ dfetch.setText(mname + " to '" + dbclass + "'");
+ rfetch.add(dfetch);
+ dfetch = new JMenu();
+ mname = null;
+ comp = 0;
+ }
}
}
});
@@ -4968,6 +5311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Left justify the whole alignment.
*/
+ @Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -4978,6 +5322,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Right justify the whole alignment.
*/
+ @Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -4993,11 +5338,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+ @Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
@@ -5006,11 +5352,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+ @Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -5020,11 +5367,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -5033,11 +5381,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -5046,21 +5395,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
viewport.setShowSequenceLogo(showSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
+ @Override
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -5068,11 +5424,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+ @Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
if (viewport.getSelectionGroup() != null)
@@ -5080,8 +5437,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
viewport.getSequenceSelection(),
viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()),
- viewport.getAlignment().getGroups());
+ viewport.getGapCharacter()), viewport.getAlignment()
+ .getGroups());
viewport.getAlignment().deleteAllGroups();
viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
@@ -5094,9 +5451,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
+ for (SequenceI s:gps[g].getSequences())
+ viewport.setSequenceColour(
+ s, col)
;
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
@@ -5107,7 +5464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* make the given alignmentPanel the currently selected tab
- *
+ *
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
@@ -5119,7 +5476,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
"Implementation error: cannot show a view from another alignment in an AlignFrame.");
}
if (tabbedPane != null
- & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
+ & alignPanels.indexOf(alignmentPanel) != tabbedPane
+ .getSelectedIndex())
{
tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
}
@@ -5137,6 +5495,7 @@ class PrintThread extends Thread
static PageFormat pf;
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();