X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ceb08ee0daab7acda3a7a9ffe8ce6ccdfc8472a7;hb=d425b0f6656de06fdb9bec6fb9ea291590ee57d2;hp=97829d4ececcf17d955f75ed1311959fe28c2322;hpb=516f7e3fd1e722cec18108fc79cff5600a0ea486;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 97829d4..ceb08ee 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 $Revision$
*/
@@ -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
@@ -691,7 +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
*/
@@ -737,13 +737,14 @@ 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
@@ -827,7 +828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @return true if any progress bars are still active
*/
@Override
@@ -880,7 +881,8 @@ 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!=null && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
try
{
@@ -961,7 +963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1057,8 +1059,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
FormatAdapter f = new FormatAdapter();
- String output = f.formatSequences(
- format,
+ String output = f.formatSequences(format,
viewport.getAlignment(), // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format),
@@ -1114,7 +1115,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1160,7 +1161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1179,7 +1180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1191,7 +1192,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1210,7 +1211,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1262,7 +1263,7 @@ 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
@@ -1308,7 +1309,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* close alignPanel2 and shuffle tabs appropriately.
- *
+ *
* @param alignPanel2
*/
public void closeView(AlignmentPanel alignPanel2)
@@ -1384,7 +1385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @return alignment objects for all views
*/
AlignmentI[] getViewAlignments()
@@ -1409,7 +1410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1445,7 +1446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1527,7 +1528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param up
* DOCUMENT ME!
*/
@@ -1539,7 +1540,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
return;
}
- viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true);
}
@@ -1627,7 +1629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1696,7 +1698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1708,7 +1710,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -1720,7 +1722,7 @@ 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.
*/
@@ -1781,8 +1783,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
int alwidth = 0;
- ArrayList newGraphGroups=new ArrayList();
- int fgroup=-1;
+ ArrayList newGraphGroups = new ArrayList();
+ int fgroup = -1;
if (newAlignment)
{
@@ -1850,13 +1852,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
newDs.clear(); // tidy up
}
- if (alignment.getAlignmentAnnotation()!=null)
+ if (alignment.getAlignmentAnnotation() != null)
{
- for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation())
+ for (AlignmentAnnotation alan : alignment
+ .getAlignmentAnnotation())
{
- if (alan.graphGroup>fgroup)
+ if (alan.graphGroup > fgroup)
{
- fgroup=alan.graphGroup;
+ fgroup = alan.graphGroup;
}
}
}
@@ -1870,17 +1873,20 @@ 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 (newann.graphGroup > -1)
{
- if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
}
- newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
}
newann.padAnnotation(alwidth);
@@ -1906,22 +1912,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int a = 0; a < sequences[i].getAnnotation().length; a++)
{
annotationAdded = true;
- newann=sequences[i].getAnnotation()[a];
+ newann = sequences[i].getAnnotation()[a];
newann.adjustForAlignment();
newann.padAnnotation(alwidth);
- if (newann.graphGroup>-1)
+ if (newann.graphGroup > -1)
{
- if (newann.graphGroup>-1)
+ if (newann.graphGroup > -1)
{
- if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null)
+ if (newGraphGroups.size() <= newann.graphGroup
+ || newGraphGroups.get(newann.graphGroup) == null)
{
- for (int q=newGraphGroups.size();q<=newann.graphGroup; q++)
+ for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
{
newGraphGroups.add(q, null);
}
- newGraphGroups.set(newann.graphGroup,new Integer(++fgroup));
+ newGraphGroups.set(newann.graphGroup, new Integer(
+ ++fgroup));
}
- newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue();
+ newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+ .intValue();
}
}
alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
@@ -1963,7 +1972,9 @@ 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
+ // TODO JAL-1145 graphGroups are not updated for sequence
+ // annotation added to several views. This may cause
+ // strangeness
alview[avnum].setAnnotationIndex(newann, a);
}
}
@@ -1973,10 +1984,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
viewport.firePropertyChange("alignment", null,
alignment.getSequences());
- if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector)alignPanels))
+ if (alignPanels != null)
+ {
+ for (AlignmentPanel ap : ((Vector) alignPanels))
+ {
+ ap.validateAnnotationDimensions(false);
+ }
+ }
+ else
{
- ap.validateAnnotationDimensions(false);
- }} else { alignPanel.validateAnnotationDimensions(false);}
+ alignPanel.validateAnnotationDimensions(false);
+ }
}
else
@@ -2036,7 +2054,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2049,7 +2067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2110,7 +2128,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2127,7 +2145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2150,7 +2168,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2174,7 +2192,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2210,7 +2228,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2222,7 +2240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2280,7 +2298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(trimRegion);
- for (SequenceGroup sg :viewport.getAlignment().getGroups())
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
@@ -2296,7 +2314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2344,7 +2362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2383,7 +2401,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2407,7 +2425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2424,7 +2442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param copyAnnotation
* if true then duplicate all annnotation, groups and settings
* @return new alignment panel, already displayed.
@@ -2435,7 +2453,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @return new alignment panel, already displayed.
@@ -2446,7 +2464,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- *
+ *
* @param viewTitle
* title of newly created view
* @param copyAnnotation
@@ -2542,7 +2560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2554,7 +2572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2584,7 +2602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
@Override
@@ -2599,7 +2617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2612,7 +2630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2648,7 +2666,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* called by key handler and the hide all/show all menu items
- *
+ *
* @param toggleSeqs
* @param toggleCols
*/
@@ -2718,7 +2736,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
@@ -2731,7 +2749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
@@ -2748,7 +2766,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
@@ -2777,7 +2795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2790,7 +2808,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2803,7 +2821,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2816,7 +2834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2829,7 +2847,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2842,7 +2860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2874,7 +2892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@@ -2891,7 +2909,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Set or clear 'Show Sequence Features'
- *
+ *
* @param evt
* DOCUMENT ME!
*/
@@ -2915,7 +2933,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2943,7 +2961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2983,7 +3001,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -2995,19 +3013,20 @@ 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(), viewport.getHiddenRepSequences()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+ viewport.getHiddenRepSequences()));
}
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3019,7 +3038,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3031,7 +3050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3043,7 +3062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3055,7 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3067,7 +3086,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3079,7 +3098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3091,7 +3110,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3127,7 +3146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3139,7 +3158,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
*/
@@ -3193,8 +3212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getColourAppliesToAllGroups())
{
-
- for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
{
if (cs == null)
{
@@ -3204,8 +3222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg, viewport
- .getHiddenRepSequences());
+ sg.cs = new ClustalxColourScheme(sg,
+ viewport.getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
@@ -3263,7 +3281,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3281,7 +3299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3299,7 +3317,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3318,7 +3336,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3337,7 +3355,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3433,7 +3451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3445,7 +3463,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3457,7 +3475,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3474,7 +3492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3490,7 +3508,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3506,7 +3524,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3523,7 +3541,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3535,7 +3553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3559,7 +3577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3608,7 +3626,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3620,7 +3638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3632,7 +3650,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3644,7 +3662,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -3656,7 +3674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param type
* DOCUMENT ME!
* @param pwType
@@ -3668,7 +3686,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
TreePanel tp;
- if (viewport.getSelectionGroup() != null)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 0)
{
if (viewport.getSelectionGroup().getSize() < 3)
{
@@ -3683,10 +3702,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s:sg.getSequences())
+ for (SequenceI _s : sg.getSequences())
{
- if (_s.getLength() < sg
- .getEndRes())
+ if (_s.getLength() < sg.getEndRes())
{
JOptionPane
.showMessageDialog(
@@ -3743,7 +3761,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param title
* DOCUMENT ME!
* @param order
@@ -3775,7 +3793,7 @@ 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
@@ -3812,7 +3830,7 @@ 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()
@@ -3828,7 +3846,7 @@ 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[];
- for (SequenceI sqa:viewport.getAlignment().getSequences())
+ for (SequenceI sqa : viewport.getAlignment().getSequences())
{
aann = sqa.getAnnotation();
for (int i = 0; aann != null && i < aann.length; i++)
@@ -3859,7 +3877,7 @@ 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
@@ -3928,7 +3946,7 @@ 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()
{
@@ -3943,7 +3961,7 @@ 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); }
*/
@@ -3953,9 +3971,9 @@ 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); } }
*/
@@ -4001,7 +4019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
@@ -4067,7 +4085,7 @@ 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
@@ -4118,7 +4136,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Generates menu items and listener event actions for web service clients
- *
+ *
*/
public void BuildWebServiceMenu()
{
@@ -4289,7 +4307,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception e)
{
- Cache.log.debug("Exception during web service menu building process.",e);
+ Cache.log
+ .debug("Exception during web service menu building process.",
+ e);
}
;
}
@@ -4307,7 +4327,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* construct any groupURL type service menu entries.
- *
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
@@ -4317,12 +4337,12 @@ 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
@@ -4349,12 +4369,12 @@ 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(
@@ -4362,7 +4382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
/**
* prototype of an automatically enabled/disabled analysis function
- *
+ *
*/
protected void setShowProductsEnabled()
{
@@ -4382,7 +4402,7 @@ 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.
@@ -4583,7 +4603,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception ex)
{
al = null;
- jalview.bin.Cache.log.debug("Exception during translation.", ex);
+ jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.",
+ "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE);
+ return;
}
if (al == null)
{
@@ -4603,7 +4629,7 @@ 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
@@ -4852,7 +4878,7 @@ 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.
*/
@@ -4893,11 +4919,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
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);
+ // 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
@@ -4906,7 +4936,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception x)
{
- Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ Cache.log
+ .debug("Exception when processing data source as T-COFFEE score file",
+ x);
tcf = null;
}
if (tcf == null)
@@ -4930,7 +4962,7 @@ 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 ==
@@ -4975,6 +5007,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception ex)
{
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);
}
}
@@ -5032,7 +5080,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
@@ -5045,7 +5093,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
@@ -5058,7 +5106,7 @@ 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)
@@ -5331,7 +5379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
@@ -5345,7 +5393,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
@@ -5360,7 +5408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
@@ -5374,7 +5422,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
@@ -5388,7 +5436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
@@ -5417,7 +5465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
@@ -5444,10 +5492,8 @@ 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 (SequenceI s:gps[g].getSequences())
- viewport.setSequenceColour(
- s, col)
- ;
+ for (SequenceI s : gps[g].getSequences())
+ viewport.setSequenceColour(s, col);
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
@@ -5457,7 +5503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* make the given alignmentPanel the currently selected tab
- *
+ *
* @param alignmentPanel
*/
public void setDisplayedView(AlignmentPanel alignmentPanel)