X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=c61c7995addc84ae5c1ec23ff2a06f0dfe6fc528;hpb=62df38e7204f2903d1b4e5aaef7762acf96f317d;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c61c799..cc57961 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,7 +35,7 @@ import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
import java.awt.dnd.*;
-
+import org.biojava.dasobert.eventmodel.*;
/**
* DOCUMENT ME!
@@ -44,7 +44,7 @@ import java.awt.dnd.*;
* @version $Revision$
*/
public class AlignFrame
- extends GAlignFrame implements DropTargetListener
+ extends GAlignFrame implements DropTargetListener, FeatureListener
{
/** DOCUMENT ME!! */
public static final int NEW_WINDOW_WIDTH = 700;
@@ -68,6 +68,7 @@ public class AlignFrame
*/
public AlignFrame(AlignmentI al)
{
+
viewport = new AlignViewport(al);
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
@@ -125,11 +126,24 @@ public class AlignFrame
});
- if (Desktop.desktop != null)
- {
- addServiceListeners();
- setGUINucleotide(al.isNucleotide());
+ if (Desktop.desktop != null)
+ {
+ addServiceListeners();
+ setGUINucleotide(al.isNucleotide());
+ }
+
+
+ if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+ {
+ wrapMenuItem.setSelected(true);
+ wrapMenuItem_actionPerformed(null);
+ }
+
}
+
+ public AlignViewport getViewport()
+ {
+ return viewport;
}
/* Set up intrinsic listeners for dynamically generated GUI bits. */
@@ -163,7 +177,6 @@ public class AlignFrame
}
;
});
-
}
public void setGUINucleotide(boolean nucleotide)
@@ -181,6 +194,58 @@ public class AlignFrame
}
}
+ public void comeBackLater(FeatureEvent evt)
+ {}
+
+ public void newFeatures(FeatureEvent evt)
+ {
+ if (evt.getFeatures().length > 0)
+ {
+ alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+ alignPanel.repaint();
+ if(featureSettings!=null)
+ featureSettings.setTableData();
+ }
+ }
+
+ Hashtable progressBars;
+ public void setProgressBar(String message, long id)
+ {
+ if(progressBars == null)
+ progressBars = new Hashtable();
+
+ JPanel progressPanel;
+ GridLayout layout = (GridLayout) statusPanel.getLayout();
+ if(progressBars.get( new Long(id) )!=null)
+ {
+ progressPanel = (JPanel)progressBars.get( new Long(id) );
+ statusPanel.remove(progressPanel);
+ progressBars.remove( progressPanel );
+ progressPanel = null;
+ if(message!=null)
+ statusBar.setText(message);
+
+ layout.setRows(layout.getRows() - 1);
+ }
+ else
+ {
+ progressPanel = new JPanel(new BorderLayout(10, 5));
+
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ layout.setRows(layout.getRows() + 1);
+ statusPanel.add(progressPanel);
+
+ progressBars.put(new Long(id), progressPanel);
+ }
+
+ validate();
+ }
+
/*
Added so Castor Mapping file can obtain Jalview Version
@@ -224,19 +289,15 @@ public class AlignFrame
public void saveAlignmentMenu_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"),
+ getProperty( "LAST_DIRECTORY"),
new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, currentFileFormat);
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ currentFileFormat,
+ false);
+
- chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save Alignment to file");
chooser.setToolTipText("Save");
@@ -286,9 +347,26 @@ public class AlignFrame
}
else
{
- String output = new FormatAdapter().formatSequences(format,
- viewport.getAlignment().
- getSequences());
+
+ String[] omitHidden = null;
+
+ if (viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ + "\nDo you want to save only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == JOptionPane.YES_OPTION)
+ omitHidden = viewport.getViewAsString(false);
+ }
+
+ String output = new FormatAdapter().formatSequences(
+ format,
+ viewport.alignment.getSequencesArray(),
+ omitHidden);
+
if (output == null)
{
return false;
@@ -319,13 +397,32 @@ public class AlignFrame
*/
protected void outputText_actionPerformed(ActionEvent e)
{
+ String [] omitHidden = null;
+
+ if(viewport.hasHiddenColumns)
+ {
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ "The Alignment contains hidden columns."
+ +"\nDo you want to output only the visible alignment?",
+ "Save / Omit Hidden Columns",
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+ if(reply==JOptionPane.YES_OPTION)
+ {
+ omitHidden = viewport.getViewAsString(false);
+ }
+ }
+
CutAndPasteTransfer cap = new CutAndPasteTransfer();
Desktop.addInternalFrame(cap,
"Alignment output - " + e.getActionCommand(), 600,
500);
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.getAlignment().
- getSequences()));
+
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ viewport.alignment.getSequencesArray(),
+ omitHidden));
}
/**
@@ -377,6 +474,21 @@ public class AlignFrame
thread.start();
}
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportFeatures(alignPanel);
+ }
+
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
+ {
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
+ viewport.alignment.getAlignmentAnnotation()
+ );
+ }
+
+
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
@@ -517,14 +629,14 @@ public class AlignFrame
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
+ if (!sg.getSequences(false).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.sequences.contains(temp))
+ if (sg.getSequences(false).contains(temp))
{
continue;
}
@@ -539,14 +651,14 @@ public class AlignFrame
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.sequences.contains(seq))
+ if (!sg.getSequences(false).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.sequences.contains(temp))
+ if (sg.getSequences(false).contains(temp))
{
continue;
}
@@ -573,83 +685,41 @@ public class AlignFrame
return;
}
- SequenceGroup sg = viewport.getSelectionGroup();
-
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+ String[] omitHidden = null;
- Hashtable orderedSeqs = new Hashtable();
- SequenceI[] seqs = new SequenceI[sg.getSize()];
-
- for (int i = 0; i < sg.getSize(); i++)
+ if (viewport.hasHiddenColumns)
{
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index + "", seq);
+ omitHidden = viewport.getViewAsString(true);
}
- int index = 0, startRes, endRes;
- char ch;
+ String output = new FormatAdapter().formatSequences(
+ "Fasta",
+ seqs,
+ omitHidden);
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = null;
- while (seq == null)
- {
- if (orderedSeqs.containsKey(index + ""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
- break;
- }
- else
- {
- index++;
- }
- }
-
- //FIND START RES
- //Returns residue following index if gap
- startRes = seq.findPosition(sg.getStartRes());
-
- //FIND END RES
- //Need to find the residue preceeding index if gap
- endRes = 0;
-
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- endRes++;
- }
- }
-
- if (endRes > 0)
+ Vector hiddenColumns = null;
+ if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
+ {
+ hiddenColumns =new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for(int i=0; i>>This is a fix for the moment, until a better solution is found!!<<<
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
@@ -864,7 +953,7 @@ public class AlignFrame
HistoryItem.HIDE));
- for (int i = 0; i < sg.sequences.size(); i++)
+ for (int i = 0; i < sg.getSize(false); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.getAlignment().findIndex(seq);
@@ -872,7 +961,7 @@ public class AlignFrame
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
// If the cut affects all sequences, remove highlighted columns
- if (sg.sequences.size() == viewport.alignment.getHeight())
+ if (sg.getSize(false) == viewport.alignment.getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
@@ -957,6 +1046,7 @@ public class AlignFrame
viewport.setSelectionGroup(null);
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.repaint();
PaintRefresher.Refresh(null, viewport.alignment);
}
@@ -1109,10 +1199,10 @@ public class AlignFrame
int end = viewport.alignment.getWidth();
if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().sequences != null
- && viewport.getSelectionGroup().sequences.size() > 0)
+ && viewport.getSelectionGroup().getSequences(true) != null
+ && viewport.getSelectionGroup().getSize(true) > 0)
{
- seqs = viewport.getSelectionGroup().sequences;
+ seqs = viewport.getSelectionGroup().getSequences(true);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes()+1;
}
@@ -1224,7 +1314,8 @@ public class AlignFrame
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+ ((ClustalxColourScheme)sg.cs).resetClustalX(
+ sg.getSequences(true), sg.getWidth());
}
sg.recalcConservation();
}
@@ -1308,16 +1399,55 @@ public class AlignFrame
*
* @param e DOCUMENT ME!
*/
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ public void wrapMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
- alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
scaleAbove.setVisible(wrapMenuItem.isSelected());
scaleLeft.setVisible(wrapMenuItem.isSelected());
scaleRight.setVisible(wrapMenuItem.isSelected());
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+ }
+
+ public void showAllSeqs_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenSeqs();
+ repaint();
+ }
+
+ public void showAllColumns_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ }
+
+ public void hideSelSequences_actionPerformed(ActionEvent e)
+ {
+ if(viewport.getSelectionGroup()==null)
+ return;
+
+ SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(
+ viewport.alignment
+ );
+
+ for(int i=0; i 0)) ||
+ (viewport.getSelectionGroup().getSize(false) < 4) &&
+ (viewport.getSelectionGroup().getSize(false) > 0)) ||
(viewport.getAlignment().getHeight() < 4))
{
JOptionPane.showInternalMessageDialog(this,
@@ -2037,15 +2160,15 @@ public class AlignFrame
TreePanel tp;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 3))
+ (viewport.getSelectionGroup().getSize(false) > 3))
{
int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.sequences.size())
+ while (s < sg.getSize(false))
{
- if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
sg.getEndRes())
{
JOptionPane.showMessageDialog(Desktop.desktop,
@@ -2060,9 +2183,7 @@ public class AlignFrame
}
title = title + " on region";
- tp = new TreePanel(viewport,
- viewport.getSelectionGroup().sequences, type, pwType,
- sg.getStartRes(), sg.getEndRes());
+ tp = new TreePanel(viewport, type, pwType);
}
else
{
@@ -2079,10 +2200,7 @@ public class AlignFrame
return;
}
- tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(), type, pwType,
- 0,
- viewport.alignment.getWidth());
+ tp = new TreePanel(viewport, type, pwType);
}
addTreeMenuItem(tp, title);
@@ -2176,12 +2294,12 @@ public class AlignFrame
SequenceI[] msa = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 1))
+ (viewport.getSelectionGroup().getSize(false) > 1))
{
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
SequenceGroup seqs = viewport.getSelectionGroup();
int sz;
- msa = new SequenceI[sz = seqs.getSize()];
+ msa = new SequenceI[sz = seqs.getSize(false)];
for (int i = 0; i < sz; i++)
{
@@ -2217,19 +2335,19 @@ public class AlignFrame
SequenceI[] msa = null;
if ( (viewport.getSelectionGroup() != null) &&
- (viewport.getSelectionGroup().getSize() > 0))
+ (viewport.getSelectionGroup().getSize(false) > 0))
{
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
SequenceGroup seqs = viewport.getSelectionGroup();
- if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
+ if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned())
{
seq = (SequenceI) seqs.getSequenceAt(0);
}
else
{
int sz;
- msa = new SequenceI[sz = seqs.getSize()];
+ msa = new SequenceI[sz = seqs.getSize(false)];
for (int i = 0; i < sz; i++)
{
@@ -2333,9 +2451,9 @@ public class AlignFrame
if (nf.getTree() != null)
{
tp = new TreePanel(viewport,
- viewport.getAlignment().getSequences(), nf,
"FromFile",
- title);
+ title,
+ nf);
tp.setSize(w,h);
@@ -2506,10 +2624,12 @@ public class AlignFrame
-
public void showTranslation_actionPerformed(ActionEvent e)
{
- int s, sSize = viewport.alignment.getHeight();
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();
+ String [] seqstring = viewport.getViewAsString(true);
+
+ int s, sSize = selection.length;
SequenceI [] newSeq = new SequenceI[sSize];
int res, resSize;
@@ -2518,7 +2638,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
for(s=0; s