X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9818e6b08c500b2dd9601ddea816fdd354e7fe89;hb=e33b171845992fd21094ba754498f9ab3d29f110;hp=bfcab9e1df652118113bd78916667cc23fe14440;hpb=d2219b397cfed501534b85976023e7045c35ff67;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bfcab9e..9818e6b 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;
@@ -127,7 +127,7 @@ import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
@@ -146,7 +146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignViewport viewport;
Vector alignPanels = new Vector();
-
+
/**
* Last format used to load or save alignments in this window
*/
@@ -159,7 +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
@@ -172,7 +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
@@ -187,7 +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
@@ -202,7 +202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* new alignment window with hidden columns
- *
+ *
* @param al
* AlignmentI
* @param hiddenColumns
@@ -221,7 +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
@@ -238,7 +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
@@ -267,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Make a new AlignFrame from exisiting alignmentPanels
- *
+ *
* @param ap
* AlignmentPanel
* @param av
@@ -335,7 +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
@@ -352,6 +352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
if (viewport.cursorMode
@@ -532,6 +533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void keyReleased(KeyEvent evt)
{
switch (evt.getKeyCode())
@@ -616,6 +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.");
@@ -624,6 +627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
System.err
@@ -637,6 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+ @Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
@@ -649,6 +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();
@@ -685,7 +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
*/
@@ -718,7 +724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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);
@@ -731,14 +737,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
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)
@@ -842,21 +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: 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"))
@@ -865,7 +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
{
@@ -902,6 +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);
@@ -915,16 +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
@@ -942,10 +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(
@@ -1039,7 +1059,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
FormatAdapter f = new FormatAdapter();
String output = f.formatSequences(
format,
- (Alignment) viewport.getAlignment(), // class cast exceptions will
+ viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format),
viewport.getColumnSelection());
@@ -1094,10 +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;
@@ -1139,10 +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,
@@ -1157,10 +1179,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void createPNG(File f)
{
alignPanel.makePNG(f);
@@ -1168,15 +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();
@@ -1185,10 +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
@@ -1196,11 +1222,13 @@ 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,
@@ -1210,6 +1238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getAlignment()).alignmentProperties);
}
+ @Override
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
@@ -1233,9 +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)
@@ -1278,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* close alignPanel2 and shuffle tabs appropriately.
- *
+ *
* @param alignPanel2
*/
public void closeView(AlignmentPanel alignPanel2)
@@ -1354,7 +1384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
@@ -1379,10 +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())
@@ -1414,10 +1445,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.redoList.size() < 1)
@@ -1495,7 +1527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param up
* DOCUMENT ME!
*/
@@ -1507,61 +1539,16 @@ 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(
+ sg.add(viewport.getAlignment().getSequenceAt(
alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
@@ -1585,9 +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++)
@@ -1642,10 +1627,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void copy_actionPerformed(ActionEvent e)
{
System.gc();
@@ -1710,10 +1696,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
paste(true);
@@ -1721,10 +1708,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
paste(false);
@@ -1732,7 +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.
*/
@@ -1793,6 +1781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
+ ArrayList newGraphGroups=new ArrayList();
+ int fgroup=-1;
if (newAlignment)
{
@@ -1860,6 +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.
@@ -1870,6 +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);
}
@@ -1889,11 +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
@@ -1933,6 +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);
}
}
@@ -1942,6 +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
@@ -2001,10 +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);
@@ -2013,10 +2049,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void delete_actionPerformed(ActionEvent evt)
{
@@ -2073,10 +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();
@@ -2089,10 +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();
@@ -2111,10 +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)
@@ -2134,10 +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();
@@ -2159,6 +2200,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.sendSelection();
}
+ @Override
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
@@ -2168,10 +2210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(true);
@@ -2179,10 +2222,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
trimAlignment(false);
@@ -2236,12 +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)))
{
@@ -2256,10 +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;
@@ -2303,10 +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;
@@ -2341,10 +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());
@@ -2364,22 +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.
@@ -2390,7 +2435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @return new alignment panel, already displayed.
@@ -2401,7 +2446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @param copyAnnotation
@@ -2483,11 +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);
@@ -2495,10 +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);
@@ -2506,10 +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());
@@ -2519,12 +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();
@@ -2533,9 +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())
@@ -2547,10 +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());
@@ -2559,10 +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());
@@ -2572,17 +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();
@@ -2591,7 +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
*/
@@ -2661,11 +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);
@@ -2673,11 +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();
@@ -2689,11 +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();
@@ -2701,12 +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());
@@ -2715,10 +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());
@@ -2727,10 +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());
@@ -2739,10 +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());
@@ -2751,10 +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());
@@ -2763,10 +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());
@@ -2775,10 +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());
@@ -2787,6 +2855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public FeatureSettings featureSettings;
+ @Override
public void featureSettings_actionPerformed(ActionEvent e)
{
if (featureSettings != null)
@@ -2805,10 +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());
@@ -2821,10 +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
@@ -2844,16 +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", "");
@@ -2870,10 +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)
@@ -2890,6 +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)
{
@@ -2900,6 +2975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.setOverviewPanel(overview);
}
+ @Override
public void textColour_actionPerformed(ActionEvent e)
{
new TextColourChooser().chooseColour(alignPanel, null);
@@ -2907,10 +2983,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
changeColour(null);
@@ -2918,22 +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());
@@ -2941,10 +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());
@@ -2952,10 +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());
@@ -2963,10 +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());
@@ -2974,10 +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());
@@ -2985,10 +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());
@@ -2996,10 +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());
@@ -3007,15 +3091,17 @@ 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());
@@ -3027,11 +3113,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* 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);
@@ -3039,10 +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());
@@ -3050,7 +3139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
*/
@@ -3103,12 +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;
@@ -3117,8 +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)
{
@@ -3176,10 +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()
@@ -3193,10 +3281,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
protected void modifyConservation_actionPerformed(ActionEvent e)
{
if (viewport.getConservationSelected()
@@ -3210,10 +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());
@@ -3228,10 +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());
@@ -3246,10 +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..."))
@@ -3291,6 +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()
@@ -3313,6 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3324,6 +3418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
radioItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -3338,10 +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());
@@ -3349,10 +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());
@@ -3360,10 +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();
@@ -3376,10 +3474,11 @@ 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();
@@ -3391,10 +3490,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3406,10 +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();
@@ -3422,10 +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);
@@ -3433,10 +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)
@@ -3456,10 +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)
@@ -3479,6 +3583,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
new PCAPanel(alignPanel);
}
+ @Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3489,6 +3594,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
@@ -3502,10 +3608,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
+ @Override
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3513,10 +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");
@@ -3524,10 +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");
@@ -3535,10 +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");
@@ -3546,7 +3656,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param type
* DOCUMENT ME!
* @param pwType
@@ -3570,13 +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
@@ -3634,7 +3743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param title
* DOCUMENT ME!
* @param order
@@ -3647,6 +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();
@@ -3665,7 +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
@@ -3679,6 +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();
@@ -3701,8 +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)
@@ -3716,10 +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)
@@ -3748,12 +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();
@@ -3787,6 +3899,7 @@ 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);
@@ -3815,7 +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()
{
@@ -3830,7 +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); }
*/
@@ -3840,9 +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); } }
*/
@@ -3888,10 +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
@@ -3953,7 +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
@@ -4004,7 +4118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
@@ -4023,6 +4137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
buildingMenu = true;
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
@@ -4046,7 +4161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
"Secondary Structure Prediction");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Disorder");
+ 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)
@@ -4121,6 +4236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
try
@@ -4131,7 +4247,7 @@ 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
@@ -4173,6 +4289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception e)
{
+ Cache.log.debug("Exception during web service menu building process.",e);
}
;
}
@@ -4190,7 +4307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* construct any groupURL type service menu entries.
- *
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
@@ -4200,12 +4317,12 @@ 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(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
- *
+ *
* }); webService.add(testAlView);
*/
// TODO: refactor to RestClient discoverer and merge menu entries for
@@ -4232,12 +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(
@@ -4245,7 +4362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
@@ -4265,7 +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.
@@ -4295,6 +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
@@ -4328,6 +4446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Runnable foo = new Runnable()
{
+ @Override
public void run()
{
final long sttime = System.currentTimeMillis();
@@ -4411,6 +4530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showProducts_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4444,6 +4564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void showTranslation_actionPerformed(ActionEvent e)
{
// /////////////////////////////
@@ -4482,7 +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
@@ -4522,22 +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();
@@ -4726,7 +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.
*/
@@ -4804,7 +4930,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
/*
* 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 ==
@@ -4852,6 +4978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void tabSelectionChanged(int index)
{
if (index > -1)
@@ -4862,6 +4989,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ @Override
public void tabbedPane_mousePressed(MouseEvent e)
{
if (SwingUtilities.isRightMouseButton(e))
@@ -4886,6 +5014,7 @@ 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(
@@ -4903,11 +5032,12 @@ 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());
@@ -4915,10 +5045,11 @@ 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());
@@ -4927,7 +5058,7 @@ 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)
@@ -4968,11 +5099,13 @@ 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
@@ -4988,12 +5121,14 @@ 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);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
String[] dbclasses = sf.getOrderedSupportedSources();
@@ -5034,11 +5169,13 @@ 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
@@ -5066,11 +5203,13 @@ 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
@@ -5111,11 +5250,13 @@ 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
@@ -5163,6 +5304,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Left justify the whole alignment.
*/
+ @Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -5173,6 +5315,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Right justify the whole alignment.
*/
+ @Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
AlignmentI al = viewport.getAlignment();
@@ -5188,11 +5331,12 @@ 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());
@@ -5201,11 +5345,12 @@ 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());
@@ -5215,11 +5360,12 @@ 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());
@@ -5228,11 +5374,12 @@ 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());
@@ -5241,23 +5388,26 @@ 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)
{
viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -5265,11 +5415,12 @@ 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)
@@ -5291,9 +5442,9 @@ 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());
@@ -5304,7 +5455,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* make the given alignmentPanel the currently selected tab
- *
+ *
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)
@@ -5335,6 +5486,7 @@ class PrintThread extends Thread
static PageFormat pf;
+ @Override
public void run()
{
PrinterJob printJob = PrinterJob.getPrinterJob();