X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9751f464fdce6b1c21824bb9ea515119f7b3d3d0;hb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;hp=a76106b5ffda293ace91e7263683cd9552c38b3f;hpb=8fc68b43785ce4b8a9d068fbec43e52b4e8cbf20;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a76106b..9751f46 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -44,7 +44,7 @@ import java.awt.dnd.*;
* @version $Revision$
*/
public class AlignFrame
- extends GAlignFrame implements ClipboardOwner, DropTargetListener
+ extends GAlignFrame implements DropTargetListener
{
/** DOCUMENT ME!! */
public static final int NEW_WINDOW_WIDTH = 700;
@@ -54,9 +54,6 @@ public class AlignFrame
AlignmentPanel alignPanel;
AlignViewport viewport;
- Vector viewports = new Vector();
- Vector alignPanels = new Vector();
-
/** DOCUMENT ME!! */
public String currentFileFormat = null;
Stack historyList = new Stack();
@@ -72,7 +69,6 @@ public class AlignFrame
public AlignFrame(AlignmentI al)
{
viewport = new AlignViewport(al);
- viewports.add(viewport);
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
@@ -88,7 +84,6 @@ public class AlignFrame
}
alignPanel = new AlignmentPanel(this, viewport);
- alignPanels.add(alignPanel);
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
@@ -195,11 +190,32 @@ public class AlignFrame
return jalview.bin.Cache.getProperty("VERSION");
}
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
public void fetchSequence_actionPerformed(ActionEvent e)
{
new SequenceFetcher(this);
}
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromText_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+ }
+
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ }
+
/**
* DOCUMENT ME!
*
@@ -542,10 +558,6 @@ public class AlignFrame
alignPanel.repaint();
}
- public void lostOwnership(Clipboard clipboard, Transferable contents)
- {
- Desktop.jalviewClipboard = null;
- }
/**
@@ -626,12 +638,16 @@ public class AlignFrame
seqs[i].setDBRef(seq.getDBRef());
seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
seqs[i].setDatasetSequence(seq.getDatasetSequence());
-
+ if(seq.getAnnotation()!=null)
+ {
+ for(int a=0; a>>This is a fix for the moment, until a better solution is found!!<<<
- FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
- fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
-
- if (title.startsWith("Copied sequences"))
- {
- newtitle = title;
- }
- else
- {
- newtitle = newtitle.concat("- from " + title);
- }
-
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
- NEW_WINDOW_HEIGHT);
}
else
{
+ alignment = viewport.getAlignment();
+
//!newAlignment
for (int i = 0; i < sequences.length; i++)
{
+
Sequence newseq = new Sequence(sequences[i].getName(),
sequences[i].getSequence(), sequences[i].getStart(),
sequences[i].getEnd());
- viewport.alignment.addSequence(newseq);
- if(sequences[i].getDatasetSequence()==null)
- {
- ////////////////////////////
- //Datset needs extension;
- /////////////////////////////
- Sequence ds = new Sequence(sequences[i].getName(),
- AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
- sequences[i].getStart(),
- sequences[i].getEnd());
- newseq.setDatasetSequence(ds);
- viewport.alignment.getDataset().addSequence(ds);
- }
- else
- {
- newseq.setDatasetSequence(sequences[i].getDatasetSequence());
- if(sequences[i].getDatasetSequence().getAnnotation()!=null)
- {
- for(int aa=0; aa>>This is a fix for the moment, until a better solution is found!!<<<
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+ if (title.startsWith("Copied sequences"))
+ {
+ newtitle = title;
+ }
+ else
+ {
+ newtitle = newtitle.concat("- from " + title);
+ }
+
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+ NEW_WINDOW_HEIGHT);
+
+ }
+
+
}
catch (Exception ex)
{
@@ -801,7 +835,7 @@ public class AlignFrame
//Jalview no longer allows deletion of residues.
//Check here whether any residues are in selection area
- if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
{
for (int i = 0; i < sg.sequences.size(); i++)
{
@@ -822,7 +856,7 @@ public class AlignFrame
j++;
}while(j<=sg.getEndRes());
}
- }
+ }*/
addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
@@ -1207,8 +1241,8 @@ public class AlignFrame
viewport.padGaps = padGapsMenuitem.isSelected();
- if (viewport.padGaps)
- alignmentChanged();
+ // if (viewport.padGaps)
+ alignmentChanged();
}
/**
@@ -1943,6 +1977,10 @@ public class AlignFrame
public void autoCalculate_actionPerformed(ActionEvent e)
{
viewport.autoCalculateConsensus = autoCalculate.isSelected();
+ if(viewport.autoCalculateConsensus)
+ {
+ alignmentChanged();
+ }
}
@@ -2355,6 +2393,7 @@ public class AlignFrame
{
// Add any Multiple Sequence Alignment Services
final JMenu msawsmenu = new JMenu("Alignment");
+ final AlignFrame af = this;
for (int i = 0, j = msaws.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2366,7 +2405,7 @@ public class AlignFrame
{
SequenceI[] msa = gatherSequencesForAlignment();
new jalview.ws.MsaWSClient(sh, title, msa,
- false, true, viewport.getAlignment().getDataset());
+ false, true, viewport.getAlignment().getDataset(), af);
}
@@ -2383,7 +2422,7 @@ public class AlignFrame
{
SequenceI[] msa = gatherSequencesForAlignment();
new jalview.ws.MsaWSClient(sh, title, msa,
- true, true, viewport.getAlignment().getDataset());
+ true, true, viewport.getAlignment().getDataset(), af);
}
@@ -2507,42 +2546,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
jalview.datamodel.AlignmentAnnotation[] annotations
= viewport.alignment.getAlignmentAnnotation();
int a, aSize;
- for (int i = 0; i < annotations.length; i++)
+ if(annotations!=null)
{
-
- if (annotations[i].label.equals("Quality") ||
- annotations[i].label.equals("Conservation") ||
- annotations[i].label.equals("Consensus"))
+ for (int i = 0; i < annotations.length; i++)
{
- continue;
- }
-
+ if (annotations[i].label.equals("Quality") ||
+ annotations[i].label.equals("Conservation") ||
+ annotations[i].label.equals("Consensus"))
+ {
+ continue;
+ }
- aSize = viewport.alignment.getWidth()/3;
- jalview.datamodel.Annotation [] anots =
- new jalview.datamodel.Annotation[aSize];
+ aSize = viewport.alignment.getWidth() / 3;
+ jalview.datamodel.Annotation[] anots =
+ new jalview.datamodel.Annotation[aSize];
- for(a=0; a