/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
package jalview.appletgui;
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
+import java.io.*;
+import java.net.*;
+import java.util.*;
+
import java.awt.*;
import java.awt.event.*;
-import java.util.*;
-import java.io.InputStreamReader;
-import java.io.BufferedReader;
-import java.net.URL;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
-public class AlignFrame extends Frame implements ActionListener,
+public class AlignFrame
+ extends Frame implements ActionListener,
ItemListener, KeyListener, MouseListener
{
public AlignmentPanel alignPanel;
public AlignViewport viewport;
- int NEW_WINDOW_WIDTH = 700;
- int NEW_WINDOW_HEIGHT = 500;
+ int DEFAULT_WIDTH = 700;
+ int DEFAULT_HEIGHT = 500;
String jalviewServletURL;
-
- public AlignFrame(AlignmentI al,
- jalview.bin.JalviewLite applet,
- String title,
- boolean embedded)
+ public AlignFrame(AlignmentI al,
+ jalview.bin.JalviewLite applet,
+ String title,
+ boolean embedded)
{
- jalviewServletURL = applet.getParameter("APPLICATION_URL");
+ if (applet != null)
+ {
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");
+ }
- try{
+ try
+ {
jbInit();
- }catch(Exception ex)
+ }
+ catch (Exception ex)
{
ex.printStackTrace();
}
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
+ viewport.updateConservation(alignPanel);
+ viewport.updateConsensus(alignPanel);
+
annotationPanelMenuItem.setState(viewport.showAnnotation);
seqLimits.setState(viewport.showJVSuffix);
- if(applet!=null)
+ if (applet != null)
{
String param = applet.getParameter("sortBy");
if (param != null)
{
if (param.equalsIgnoreCase("Id"))
+ {
sortIDMenuItem_actionPerformed();
+ }
else if (param.equalsIgnoreCase("Pairwise Identity"))
+ {
sortPairwiseMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
if (param != null)
{
int width = Integer.parseInt(param);
- NEW_WINDOW_WIDTH = width;
+ DEFAULT_WIDTH = width;
}
param = applet.getParameter("windowHeight");
if (param != null)
{
int height = Integer.parseInt(param);
- NEW_WINDOW_HEIGHT = height;
+ DEFAULT_HEIGHT = height;
}
}
catch (Exception ex)
}
- //Some JVMS send keyevents to Top frame or lowest panel,
- //Havent worked out why yet. So add to both this frame and seqCanvas for now
- this.addKeyListener(this);
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);
- alignPanel.idPanel.idCanvas.addKeyListener(this);
- alignPanel.scalePanel.addKeyListener(this);
- alignPanel.annotationPanel.addKeyListener(this);
+ //Some JVMS send keyevents to Top frame or lowest panel,
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now
+ this.addKeyListener(this);
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);
+ alignPanel.idPanel.idCanvas.addKeyListener(this);
+ alignPanel.scalePanel.addKeyListener(this);
+ alignPanel.annotationPanel.addKeyListener(this);
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ if (embedded)
{
- public void propertyChange(java.beans.PropertyChangeEvent evt)
- {
- if (evt.getPropertyName().equals("alignment"))
- {
- alignmentChanged();
- }
- }
- });
-
-
- if(embedded)
- {
- setEmbedded();
- }
- else
- {
- add(alignPanel, BorderLayout.CENTER);
- jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,
- NEW_WINDOW_HEIGHT);
- }
- alignPanel.validate();
- alignPanel.repaint();
+ setEmbedded();
+ }
+ else
+ {
+ add(alignPanel, BorderLayout.CENTER);
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ alignPanel.validate();
+ alignPanel.paintAlignment(true);
}
+
public AlignViewport getAlignViewport()
{
return viewport;
return alignPanel.seqPanel.seqCanvas;
}
-
/**
* DOCUMENT ME!
*
{
Hashtable featureLinks = new Hashtable();
boolean featuresFile = false;
- try{
- featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- featureLinks,
- true);
+ try
+ {
+ featuresFile = new jalview.io.FeaturesFile(file,
+ type).parse(viewport.alignment,
+ alignPanel.seqPanel.seqCanvas.
+ getFeatureRenderer().featureColours,
+ featureLinks,
+ true);
}
- catch(Exception ex)
+ catch (Exception ex)
{
ex.printStackTrace();
}
- if(featuresFile)
+ if (featuresFile)
{
- if(featureLinks.size()>0)
+ if (featureLinks.size() > 0)
+ {
alignPanel.seqPanel.seqCanvas
.getFeatureRenderer().featureLinks = featureLinks;
+ }
viewport.showSequenceFeatures = true;
sequenceFeatures.setState(true);
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
}
-
public void keyPressed(KeyEvent evt)
{
- if (viewport.cursorMode
- && evt.getKeyCode() >= KeyEvent.VK_0
- && evt.getKeyCode() <= KeyEvent.VK_9)
- {
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());
- }
+ if (viewport.cursorMode &&
+ ( (evt.getKeyCode() >= KeyEvent.VK_0 &&
+ evt.getKeyCode() <= KeyEvent.VK_9)
+ ||
+ (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&
+ evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)
+ )
+ && Character.isDigit(evt.getKeyChar()))
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+
switch (evt.getKeyCode())
{
}
break;
case KeyEvent.VK_V:
- if (evt.isControlDown() || evt.isMetaDown())
+ if (evt.isControlDown())
{
- paste(true);
+ paste(evt.isShiftDown());
}
break;
case KeyEvent.VK_A:
}
break;
case KeyEvent.VK_DOWN:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
- alignPanel.seqPanel.moveCursor(0,1);
+ alignPanel.seqPanel.moveCursor(0, 1);
}
else
+ {
moveSelectedSequences(false);
+ }
break;
case KeyEvent.VK_UP:
if (viewport.cursorMode)
{
- alignPanel.seqPanel.moveCursor(0,-1);
+ alignPanel.seqPanel.moveCursor(0, -1);
}
else
+ {
moveSelectedSequences(true);
+ }
break;
case KeyEvent.VK_LEFT:
- if(viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(-1,0);
- }
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false,
+ alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor( -1, 0);
break;
case KeyEvent.VK_RIGHT:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(1,0);
- }
- break;
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true,
+ alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor( 1, 0);
+ break;
+
case KeyEvent.VK_SPACE:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown()
+ );
}
break;
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown()
+ || evt.isAltDown());
}
- else
+ else
{
cut_actionPerformed();
alignPanel.seqPanel.seqCanvas.repaint();
break;
case KeyEvent.VK_S:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorRow();
}
break;
case KeyEvent.VK_P:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorPosition();
}
case KeyEvent.VK_ENTER:
case KeyEvent.VK_COMMA:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.setCursorRowAndColumn();
}
break;
case KeyEvent.VK_Q:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.setSelectionAreaAtCursor(true);
}
break;
case KeyEvent.VK_M:
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
alignPanel.seqPanel.setSelectionAreaAtCursor(false);
}
break;
- case KeyEvent.VK_F2:
- viewport.cursorMode = ! viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is "+
- (viewport.cursorMode ? "on" : "off"));
- if(viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- alignPanel.seqPanel.seqCanvas.repaint();
- break;
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText("Keyboard editing mode is " +
+ (viewport.cursorMode ? "on" : "off"));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ break;
case KeyEvent.VK_F:
if (evt.isControlDown())
findMenuItem_actionPerformed();
}
break;
+
case KeyEvent.VK_H:
{
boolean toggleSeqs = !evt.isControlDown();
boolean hide = false;
SequenceGroup sg = viewport.getSelectionGroup();
- if(toggleSeqs)
+ if (toggleSeqs)
{
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
{
hide = true;
viewport.hideAllSelectedSeqs();
}
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
viewport.showAllHiddenSeqs();
+ }
}
- if(toggleCols)
+ if (toggleCols)
{
if (viewport.colSel.getSelected().size() > 0)
{
viewport.hideSelectedColumns();
- if(!toggleSeqs)
- viewport.selectionGroup = sg;
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
}
else if (!hide)
+ {
viewport.showAllHiddenColumns();
+ }
}
-
- alignPanel.repaint();
break;
}
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes,
+ viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_Z:
+ if (evt.isControlDown())
+ {
+ undoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_Y:
+ if (evt.isControlDown())
+ {
+ redoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_L:
+ if (evt.isControlDown())
+ {
+ trimAlignment(true);
+ }
+ break;
+
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
+
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.removeAllGapsMenuItem_actionPerformed();
+ }
+ else
+ {
+ removeGappedColumnMenuItem_actionPerformed();
+ }
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
+ {
+ viewport.invertColumnSelection();
+ }
+ else
+ {
+ this.invertSequenceMenuItem_actionPerformed();
+ }
+ }
+ break;
+
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView();
+ }
+ break;
+
}
+ alignPanel.paintAlignment(true);
}
+
public void keyReleased(KeyEvent evt)
{}
+
public void keyTyped(KeyEvent evt)
{}
-public void itemStateChanged(ItemEvent evt)
- {
- if(evt.getSource()==colourTextMenuItem)
- colourTextMenuItem_actionPerformed();
- else if(evt.getSource()==wrapMenuItem)
- wrapMenuItem_actionPerformed();
- else if(evt.getSource()==scaleAbove)
- scaleAbove_actionPerformed();
- else if(evt.getSource()==scaleLeft)
- scaleLeft_actionPerformed();
- else if(evt.getSource()==scaleRight)
- scaleRight_actionPerformed();
- else if(evt.getSource()==seqLimits)
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == colourTextMenuItem)
+ {
+ colourTextMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == wrapMenuItem)
+ {
+ wrapMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == scaleAbove)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
+ }
+ else if (evt.getSource() == scaleLeft)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.getState());
+ }
+ else if (evt.getSource() == scaleRight)
+ {
+ viewport.setScaleRightWrapped(scaleRight.getState());
+ }
+ else if (evt.getSource() == seqLimits)
+ {
seqLimits_itemStateChanged();
- else if(evt.getSource()==viewBoxesMenuItem)
- viewBoxesMenuItem_actionPerformed();
- else if(evt.getSource()==viewTextMenuItem)
- viewTextMenuItem_actionPerformed();
- else if(evt.getSource()==renderGapsMenuItem)
- renderGapsMenuItem_actionPerformed();
- else if(evt.getSource()==annotationPanelMenuItem)
- annotationPanelMenuItem_actionPerformed();
- else if(evt.getSource()==sequenceFeatures)
- {
- viewport.showSequenceFeatures(sequenceFeatures.getState());
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- else if(evt.getSource()==conservationMenuItem)
- conservationMenuItem_actionPerformed();
- else if(evt.getSource()==abovePIDThreshold)
- abovePIDThreshold_actionPerformed();
- else if(evt.getSource()==applyToAllGroups)
- applyToAllGroups_actionPerformed();
- else if(evt.getSource()==autoCalculate)
- viewport.autocalculateConsensus = autoCalculate.getState();
- }
- public void actionPerformed(ActionEvent evt)
- {
+ }
+ else if (evt.getSource() == viewBoxesMenuItem)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());
+ }
+ else if (evt.getSource() == viewTextMenuItem)
+ {
+ viewport.setShowText(viewTextMenuItem.getState());
+ }
+ else if (evt.getSource() == renderGapsMenuItem)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.getState());
+ }
+ else if (evt.getSource() == annotationPanelMenuItem)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ }
+ else if (evt.getSource() == sequenceFeatures)
+ {
+ viewport.showSequenceFeatures(sequenceFeatures.getState());
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ else if (evt.getSource() == conservationMenuItem)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == abovePIDThreshold)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ else if (evt.getSource() == applyToAllGroups)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
+ }
+ else if (evt.getSource() == autoCalculate)
+ {
+ viewport.autocalculateConsensus = autoCalculate.getState();
+ }
+
+ alignPanel.paintAlignment(true);
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
Object source = evt.getSource();
- if(source==inputText)
+ if (source == inputText)
+ {
inputText_actionPerformed();
- else if(source==loadTree)
+ }
+ else if (source == loadTree)
+ {
loadTree_actionPerformed();
- else if(source==loadApplication)
+ }
+ else if (source == loadApplication)
+ {
launchFullApplication();
- else if(source==closeMenuItem)
+ }
+ else if (source == loadAnnotations)
+ {
+ loadAnnotations();
+ }
+ else if (source == outputAnnotations)
+ {
+ outputAnnotations(true);
+ }
+ else if (source == outputFeatures)
+ {
+ outputFeatures(true, "Jalview");
+ }
+ else if (source == closeMenuItem)
+ {
closeMenuItem_actionPerformed();
- else if(source==copy)
+ }
+ else if (source == copy)
+ {
copy_actionPerformed();
- else if(source==undoMenuItem)
+ }
+ else if (source == undoMenuItem)
+ {
undoMenuItem_actionPerformed();
- else if(source==redoMenuItem)
+ }
+ else if (source == redoMenuItem)
+ {
redoMenuItem_actionPerformed();
- else if(source==inputText)
- inputText_actionPerformed();
- else if(source==closeMenuItem)
- closeMenuItem_actionPerformed();
- else if(source==undoMenuItem)
- undoMenuItem_actionPerformed();
- else if(source==redoMenuItem)
- redoMenuItem_actionPerformed();
- else if(source==copy)
- copy_actionPerformed();
- else if(source==pasteNew)
- pasteNew_actionPerformed();
- else if(source==pasteThis)
- pasteThis_actionPerformed();
- else if(source==cut)
- cut_actionPerformed();
- else if(source==delete)
- delete_actionPerformed();
- else if(source==deleteGroups)
- deleteGroups_actionPerformed();
- else if(source==selectAllSequenceMenuItem)
- selectAllSequenceMenuItem_actionPerformed();
- else if(source==deselectAllSequenceMenuItem)
- deselectAllSequenceMenuItem_actionPerformed();
- else if(source==invertSequenceMenuItem)
- invertSequenceMenuItem_actionPerformed();
- else if(source==invertColSel)
- { viewport.invertColumnSelection(); alignPanel.repaint(); }
- else if(source==remove2LeftMenuItem)
- remove2LeftMenuItem_actionPerformed();
- else if(source==remove2RightMenuItem)
- remove2RightMenuItem_actionPerformed();
- else if(source==removeGappedColumnMenuItem)
- removeGappedColumnMenuItem_actionPerformed();
- else if(source==removeAllGapsMenuItem)
- removeAllGapsMenuItem_actionPerformed();
- else if(source==findMenuItem)
- findMenuItem_actionPerformed();
- else if(source==font)
- font_actionPerformed();
- else if(source==showColumns)
+ }
+ else if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == closeMenuItem)
+ {
+ closeMenuItem_actionPerformed();
+ }
+ else if (source == undoMenuItem)
+ {
+ undoMenuItem_actionPerformed();
+ }
+ else if (source == redoMenuItem)
+ {
+ redoMenuItem_actionPerformed();
+ }
+ else if (source == copy)
+ {
+ copy_actionPerformed();
+ }
+ else if (source == pasteNew)
+ {
+ pasteNew_actionPerformed();
+ }
+ else if (source == pasteThis)
+ {
+ pasteThis_actionPerformed();
+ }
+ else if (source == cut)
+ {
+ cut_actionPerformed();
+ }
+ else if (source == delete)
+ {
+ delete_actionPerformed();
+ }
+ else if (source == deleteGroups)
+ {
+ deleteGroups_actionPerformed();
+ }
+ else if (source == selectAllSequenceMenuItem)
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == deselectAllSequenceMenuItem)
+ {
+ deselectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertSequenceMenuItem)
+ {
+ invertSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertColSel)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == remove2LeftMenuItem)
+ {
+ trimAlignment(true);
+ }
+ else if (source == remove2RightMenuItem)
+ {
+ trimAlignment(false);
+ }
+ else if (source == removeGappedColumnMenuItem)
+ {
+ removeGappedColumnMenuItem_actionPerformed();
+ }
+ else if (source == removeAllGapsMenuItem)
+ {
+ removeAllGapsMenuItem_actionPerformed();
+ }
+ else if (source == findMenuItem)
{
- viewport.showAllHiddenColumns(); alignPanel.repaint();
+ findMenuItem_actionPerformed();
}
- else if(source==showSeqs)
+ else if (source == font)
+ {
+ new FontChooser(alignPanel);
+ }
+ else if (source == newView)
+ {
+ newView();
+ }
+ else if (source == showColumns)
+ {
+ viewport.showAllHiddenColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
}
- else if(source == hideColumns)
+ else if (source == hideColumns)
{
- viewport.hideSelectedColumns(); alignPanel.repaint();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
}
- else if(source == hideSequences && viewport.getSelectionGroup()!=null)
+ else if (source == hideSequences && viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
}
- else if(source==featureSettings)
- featureSettings_actionPerformed();
- else if(source==overviewMenuItem)
- overviewMenuItem_actionPerformed();
- else if(source==noColourmenuItem)
- noColourmenuItem_actionPerformed();
- else if(source==clustalColour)
- clustalColour_actionPerformed();
- else if(source==zappoColour)
- zappoColour_actionPerformed();
- else if(source==taylorColour)
- taylorColour_actionPerformed();
- else if(source==hydrophobicityColour)
- hydrophobicityColour_actionPerformed();
- else if(source==helixColour)
- helixColour_actionPerformed();
- else if(source==strandColour)
- strandColour_actionPerformed();
- else if(source==turnColour)
- turnColour_actionPerformed();
- else if(source==buriedColour)
- buriedColour_actionPerformed();
- else if(source==nucleotideColour)
- nucleotideColour_actionPerformed();
- else if(source==modifyPID)
- modifyPID_actionPerformed();
- else if(source==modifyConservation)
- modifyConservation_actionPerformed();
- else if(source==userDefinedColour)
- userDefinedColour_actionPerformed();
- else if(source==PIDColour)
- PIDColour_actionPerformed();
- else if(source==BLOSUM62Colour)
- BLOSUM62Colour_actionPerformed();
- else if(source==annotationColour)
- new AnnotationColourChooser(viewport, alignPanel);
- else if(source==sortPairwiseMenuItem)
- sortPairwiseMenuItem_actionPerformed();
- else if(source==sortIDMenuItem)
- sortIDMenuItem_actionPerformed();
- else if(source==sortGroupMenuItem)
- sortGroupMenuItem_actionPerformed();
- else if(source==removeRedundancyMenuItem)
- removeRedundancyMenuItem_actionPerformed();
- else if(source==pairwiseAlignmentMenuItem)
- pairwiseAlignmentMenuItem_actionPerformed();
- else if(source==PCAMenuItem)
- PCAMenuItem_actionPerformed();
- else if(source==averageDistanceTreeMenuItem)
- averageDistanceTreeMenuItem_actionPerformed();
- else if(source==neighbourTreeMenuItem)
- neighbourTreeMenuItem_actionPerformed();
- else if(source==njTreeBlosumMenuItem)
- njTreeBlosumMenuItem_actionPerformed();
- else if(source==avDistanceTreeBlosumMenuItem)
- avTreeBlosumMenuItem_actionPerformed();
- else if(source==documentation)
- documentation_actionPerformed();
- else if(source==about)
- about_actionPerformed();
-
- }
+ else if (source == featureSettings)
+ {
+ new FeatureSettings(alignPanel);
+ }
+ else if(source== alProperties)
+ {
+ StringBuffer contents = new StringBuffer();
+
+ float avg = 0;
+ int min=Integer.MAX_VALUE, max=0;
+ for(int i=0; i<viewport.alignment.getHeight(); i++)
+ {
+ int size = viewport.alignment.getSequenceAt(i).getEnd()
+ -viewport.alignment.getSequenceAt(i).getStart();
+ avg += size;
+ if(size>max)
+ max = size;
+ if(size<min)
+ min = size;
+ }
+ avg = avg/(float)viewport.alignment.getHeight();
+
+ contents.append("\nSequences: "+ viewport.alignment.getHeight());
+ contents.append("\nMinimum Sequence Length: "+min);
+ contents.append("\nMaximum Sequence Length: "+max);
+ contents.append("\nAverage Length: "+(int)avg);
+
+ if (((Alignment)viewport.alignment).alignmentProperties != null)
+ {
+ Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;
+ Enumeration en = props.keys();
+ while(en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ contents.append("\n"+key+"\t"+props.get(key));
+ }
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ cap.setText(contents.toString());
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Alignment Properties: "+getTitle()
+ , 400, 250);
+ }
+ else if (source == overviewMenuItem)
+ {
+ overviewMenuItem_actionPerformed();
+ }
+ else if (source == noColourmenuItem)
+ {
+ changeColour(null);
+ }
+ else if (source == clustalColour)
+ {
+ abovePIDThreshold.setState(false);
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
+ viewport.alignment.getWidth()));
+ }
+ else if (source == zappoColour)
+ {
+ changeColour(new ZappoColourScheme());
+ }
+ else if (source == taylorColour)
+ {
+ changeColour(new TaylorColourScheme());
+ }
+ else if (source == hydrophobicityColour)
+ {
+ changeColour(new HydrophobicColourScheme());
+ }
+ else if (source == helixColour)
+ {
+ changeColour(new HelixColourScheme());
+ }
+ else if (source == strandColour)
+ {
+ changeColour(new StrandColourScheme());
+ }
+ else if (source == turnColour)
+ {
+ changeColour(new TurnColourScheme());
+ }
+ else if (source == buriedColour)
+ {
+ changeColour(new BuriedColourScheme());
+ }
+ else if (source == nucleotideColour)
+ {
+ changeColour(new NucleotideColourScheme());
+ }
+ else if (source == modifyPID)
+ {
+ modifyPID_actionPerformed();
+ }
+ else if (source == modifyConservation)
+ {
+ modifyConservation_actionPerformed();
+ }
+ else if (source == userDefinedColour)
+ {
+ new UserDefinedColours(alignPanel, null);
+ }
+ else if (source == PIDColour)
+ {
+ changeColour(new PIDColourScheme());
+ }
+ else if (source == BLOSUM62Colour)
+ {
+ changeColour(new Blosum62ColourScheme());
+ }
+ else if (source == annotationColour)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+ else if (source == sortPairwiseMenuItem)
+ {
+ sortPairwiseMenuItem_actionPerformed();
+ }
+ else if (source == sortIDMenuItem)
+ {
+ sortIDMenuItem_actionPerformed();
+ }
+ else if (source == sortGroupMenuItem)
+ {
+ sortGroupMenuItem_actionPerformed();
+ }
+ else if (source == removeRedundancyMenuItem)
+ {
+ removeRedundancyMenuItem_actionPerformed();
+ }
+ else if (source == pairwiseAlignmentMenuItem)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed();
+ }
+ else if (source == PCAMenuItem)
+ {
+ PCAMenuItem_actionPerformed();
+ }
+ else if (source == averageDistanceTreeMenuItem)
+ {
+ averageDistanceTreeMenuItem_actionPerformed();
+ }
+ else if (source == neighbourTreeMenuItem)
+ {
+ neighbourTreeMenuItem_actionPerformed();
+ }
+ else if (source == njTreeBlosumMenuItem)
+ {
+ njTreeBlosumMenuItem_actionPerformed();
+ }
+ else if (source == avDistanceTreeBlosumMenuItem)
+ {
+ avTreeBlosumMenuItem_actionPerformed();
+ }
+ else if (source == documentation)
+ {
+ documentation_actionPerformed();
+ }
+ else if (source == about)
+ {
+ about_actionPerformed();
+ }
+
+ }
public void inputText_actionPerformed()
{
protected void outputText_actionPerformed(ActionEvent e)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame,
"Alignment output - " + e.getActionCommand(),
600, 500);
cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),
- viewport.getAlignment().getSequences(),
- viewport.showJVSuffix));
+ viewport.getAlignment(),
+ viewport.showJVSuffix));
+ }
+
+ public void loadAnnotations()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ cap.setText("Paste your features / annotations file here.");
+ cap.setAnnotationImport();
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
+
+ }
+
+ public String outputAnnotations(boolean displayTextbox)
+ {
+ String annotation = new AnnotationFile().printAnnotations(
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+ viewport.alignment.getGroups(),
+ ((Alignment) viewport.alignment).alignmentProperties);
+
+ if (displayTextbox)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Annotations",
+ 600, 500);
+ cap.setText(annotation);
+ }
+
+ return annotation;
+ }
+
+ public String outputFeatures(boolean displayTextbox, String format)
+ {
+ String features;
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = new FeaturesFile().printJalviewFormat(
+ viewport.alignment.getSequencesArray(),
+ viewport.featuresDisplayed);
+ }
+ else
+ {
+ features = new FeaturesFile().printGFFFormat(
+ viewport.alignment.getSequencesArray(),
+ viewport.featuresDisplayed);
+ }
+
+ if (displayTextbox)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Features",
+ 600, 500);
+
+ cap.setText(features);
+ }
+
+ return features;
}
void launchFullApplication()
{
StringBuffer url = new StringBuffer(jalviewServletURL);
- url.append("?open="+
- appendProtocol( viewport.applet.getParameter("file") ) );
+ url.append("?open=" +
+ appendProtocol(viewport.applet.getParameter("file")));
+
+ if (viewport.applet.getParameter("features") != null)
+ {
+ url.append("&features=");
+ url.append(appendProtocol(viewport.applet.getParameter("features")));
+ }
- if(viewport.applet.getParameter("features")!=null)
+ if (viewport.applet.getParameter("annotations") != null)
{
- url.append( "&features=" );
- url.append( appendProtocol( viewport.applet.getParameter("features") ) );
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));
}
- if(viewport.applet.getParameter("annotations")!=null)
+ if (viewport.applet.getParameter("jnetfile") != null)
{
- url.append( "&annotations=" );
- url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
}
- if(viewport.applet.getParameter("defaultColour")!=null)
+ if (viewport.applet.getParameter("defaultColour") != null)
{
url.append("&colour=" +
removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
);
}
- if(viewport.applet.getParameter("userDefinedColour")!=null)
+ if (viewport.applet.getParameter("userDefinedColour") != null)
{
- url.append( "&colour=" +
- removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )
- );
+ url.append("&colour=" +
+ removeWhiteSpace(viewport.applet.getParameter(
+ "userDefinedColour"))
+ );
}
showURL(url.toString(), "FULL_APP");
}
-
String removeWhiteSpace(String colour)
{
StringBuffer sb = new StringBuffer();
for (int i = 0; i < colour.length(); i++)
{
if (Character.isWhitespace(colour.charAt(i)))
+ {
sb.append("%20");
+ }
else
+ {
sb.append(colour.charAt(i));
+ }
}
return sb.toString();
}
-
String appendProtocol(String url)
{
- try{
- new URL(url);
- }catch(java.net.MalformedURLException ex)
+ try
+ {
+ new URL(url);
+ }
+ catch (java.net.MalformedURLException ex)
{
- url = viewport.applet.getCodeBase()+url;
+ url = viewport.applet.getCodeBase() + url;
}
return url;
}
public void closeMenuItem_actionPerformed()
{
- PaintRefresher.components.remove(viewport.alignment);
- if(PaintRefresher.components.size()==0 && viewport.applet==null)
+ PaintRefresher.RemoveComponent(alignPanel);
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)
+ {
System.exit(0);
+ }
this.dispose();
}
- Stack historyList = new Stack();
- Stack redoList = new Stack();
-
+ /**
+ * DOCUMENT ME!
+ */
void updateEditMenuBar()
{
- if (historyList.size() > 0)
+
+ if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem) historyList.peek();
- undoMenuItem.setLabel("Undo " + hi.getDescription());
+ CommandI command = (CommandI) viewport.historyList.peek();
+ undoMenuItem.setLabel("Undo " + command.getDescription());
}
else
{
undoMenuItem.setLabel("Undo");
}
- if (redoList.size() > 0)
+ if (viewport.redoList.size() > 0)
{
redoMenuItem.setEnabled(true);
- HistoryItem hi = (HistoryItem) redoList.peek();
- redoMenuItem.setLabel("Redo " + hi.getDescription());
+
+ CommandI command = (CommandI) viewport.redoList.peek();
+ redoMenuItem.setLabel("Redo " + command.getDescription());
}
else
{
}
}
- public void addHistoryItem(HistoryItem hi)
+ public void addHistoryItem(CommandI command)
{
- historyList.push(hi);
- redoList.clear();
- updateEditMenuBar();
+ if (command.getSize() > 0)
+ {
+ viewport.historyList.push(command);
+ viewport.redoList.removeAllElements();
+ updateEditMenuBar();
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ }
}
-
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void undoMenuItem_actionPerformed()
{
- HistoryItem nh,hi = (HistoryItem) historyList.pop();
- redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
- HistoryItem.HIDE));
- if (hi.alColumnChanges!=null)
- nh.alColumnChanges=hi.alColumnChanges.getInverse();
- restoreHistoryItem(hi);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ if (viewport.historyList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.historyList.pop();
+ viewport.redoList.push(command);
+ command.undoCommand(null);
+
+ AlignViewport originalSource = getOriginatingSource(command);
+
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ updateEditMenuBar();
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.alignment.getSequences());
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
protected void redoMenuItem_actionPerformed()
{
- HistoryItem nh,hi = (HistoryItem) redoList.pop();
- historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
- HistoryItem.HIDE));
- if (hi.alColumnChanges!=null)
- nh.alColumnChanges=hi.alColumnChanges.getInverse();
- restoreHistoryItem(hi);
+ if (viewport.redoList.size() < 1)
+ {
+ return;
+ }
+
+ CommandI command = (CommandI) viewport.redoList.pop();
+ viewport.historyList.push(command);
+ command.doCommand(null);
+
+ AlignViewport originalSource = getOriginatingSource(command);
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+
updateEditMenuBar();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ originalSource.firePropertyChange("alignment", null,
+ originalSource.alignment.getSequences());
}
- // used by undo and redo
- void restoreHistoryItem(HistoryItem hi)
+ AlignViewport getOriginatingSource(CommandI command)
{
- hi.restore(viewport.getColumnSelection());
- updateEditMenuBar();
+ AlignViewport originalSource = null;
+ //For sequence removal and addition, we need to fire
+ //the property change event FROM the viewport where the
+ //original alignment was altered
+ AlignmentI al = null;
+ if (command instanceof EditCommand)
+ {
+ EditCommand editCommand = (EditCommand) command;
+ al = editCommand.getAlignment();
+ Vector comps = (Vector) PaintRefresher.components
+ .get(viewport.getSequenceSetId());
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+ {
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+
+ if (originalSource == null)
+ {
+ //The original view is closed, we must validate
+ //the current view against the closed view first
+ if (al != null)
+ {
+ PaintRefresher.validateSequences(al, viewport.alignment);
+ }
+
+ originalSource = viewport;
+ }
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ return originalSource;
}
public void moveSelectedSequences(boolean up)
for (int i = 1; i < viewport.alignment.getHeight(); i++)
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(false).contains(seq))
+ if (!sg.getSequences(null).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(false).contains(temp))
+ if (sg.getSequences(null).contains(temp))
{
continue;
}
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
{
SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(true).contains(seq))
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
{
continue;
}
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(true).contains(temp))
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
{
continue;
}
}
}
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
+ }
+
+ synchronized void slideSequences(boolean right, int size)
+ {
+ Vector sg = new Vector();
+ if(viewport.cursorMode)
+ {
+ sg.addElement(viewport.alignment.getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if(viewport.getSelectionGroup()!=null
+ && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
+ {
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.hiddenRepSequences);
+ }
+
+ if(sg.size()<1)
+ {
+ return;
+ }
+
+ Vector invertGroup = new Vector();
+
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)
+ {
+ if(!sg.contains(viewport.alignment.getSequenceAt(i)))
+ invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+ }
+
+ SequenceI[] seqs1 = new SequenceI[sg.size()];
+ for (int i = 0; i < sg.size(); i++)
+ seqs1[i] = (SequenceI) sg.elementAt(i);
+
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+ for (int i = 0; i < invertGroup.size(); i++)
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+
+ SlideSequencesCommand ssc;
+ if (right)
+ ssc = new SlideSequencesCommand("Slide Sequences",
+ seqs2, seqs1, size,
+ viewport.getGapCharacter()
+ );
+ else
+ ssc = new SlideSequencesCommand("Slide Sequences",
+ seqs1, seqs2, size,
+ viewport.getGapCharacter()
+ );
+
+ int groupAdjustment = 0;
+ if (ssc.getGapsInsertedBegin() && right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor(size, 0);
+ else
+ groupAdjustment = size;
+ }
+ else if (!ssc.getGapsInsertedBegin() && !right)
+ {
+ if (viewport.cursorMode)
+ alignPanel.seqPanel.moveCursor( -size, 0);
+ else
+ groupAdjustment = -size;
+ }
+
+ if (groupAdjustment != 0)
+ {
+ viewport.getSelectionGroup().setStartRes(
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().setEndRes(
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ }
+
+
+ boolean appendHistoryItem = false;
+ if(viewport.historyList!=null
+ && viewport.historyList.size()>0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ {
+ appendHistoryItem = ssc.appendSlideCommand(
+ (SlideSequencesCommand)viewport.historyList.peek())
+ ;
+ }
+
+ if(!appendHistoryItem)
+ addHistoryItem(ssc);
+
+ repaint();
}
static StringBuffer copiedSequences;
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
Hashtable orderedSeqs = new Hashtable();
- for (int i = 0; i < sg.getSize(false); i++)
+ for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
int index = viewport.alignment.findIndex(seq);
viewport.getColumnSelection().getHiddenColumns().elementAt(i);
copiedHiddenColumns.addElement(new int[]
- {region[0] - hiddenOffset,
- region[1] - hiddenOffset});
+ {region[0] - hiddenOffset,
+ region[1] - hiddenOffset});
}
}
else
+ {
copiedHiddenColumns = null;
+ }
-
- for (int i = 0; i < sg.getSize(false); i++)
+ for (int i = 0; i < sg.getSize(); i++)
{
- SequenceI seq = null;
+ SequenceI seq = null;
- while (seq == null)
+ while (seq == null)
+ {
+ if (orderedSeqs.containsKey(index + ""))
{
- if (orderedSeqs.containsKey(index + ""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
+ seq = (SequenceI) orderedSeqs.get(index + "");
+ index++;
- break;
- }
- else
- {
- index++;
- }
+ break;
}
-
- //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++)
+ else
{
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap( (ch)))
- {
- endRes++;
- }
+ index++;
}
+ }
+
+ //FIND START RES
+ //Returns residue following index if gap
+ startRes = seq.findPosition(sg.getStartRes());
- if(endRes>0)
+ //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 += seq.getStart() -1;
+ endRes++;
}
+ }
+
+ if (endRes > 0)
+ {
+ endRes += seq.getStart() - 1;
+ }
- copiedSequences.append(seq.getName() + "\t" +
- startRes + "\t" +
- endRes + "\t" +
- seq.getSequence(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
+ copiedSequences.append(seq.getName() + "\t" +
+ startRes + "\t" +
+ endRes + "\t" +
+ seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
}
}
protected void pasteThis_actionPerformed()
{
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
- HistoryItem.PASTE));
paste(false);
}
{
try
{
+
if (copiedSequences == null)
{
return;
String name = st.nextToken();
int start = Integer.parseInt(st.nextToken());
int end = Integer.parseInt(st.nextToken());
- Sequence sequence = new Sequence(name, st.nextToken(), start, end);
-
- if (!newAlignment)
- {
- viewport.alignment.addSequence(sequence);
- }
- else
- {
- seqs.addElement(sequence);
- }
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));
+ }
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);
}
if (newAlignment)
{
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- newSeqs[i] = (SequenceI) seqs.elementAt(i);
- }
-
String newtitle = new String("Copied sequences");
if (getTitle().startsWith("Copied sequences"))
{
}
}
-
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,
- NEW_WINDOW_HEIGHT);
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
}
else
{
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ addSequences(newSeqs);
}
}
}
+ void addSequences(SequenceI[] seqs)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ viewport.alignment.addSequence(seqs[i]);
+ }
+
+ //!newAlignment
+ addHistoryItem(new EditCommand(
+ "Add sequences",
+ EditCommand.PASTE,
+ seqs,
+ 0,
+ viewport.alignment.getWidth(),
+ viewport.alignment)
+ );
+
+ viewport.setEndSeq(viewport.alignment.getHeight());
+ viewport.alignment.getWidth();
+ viewport.firePropertyChange("alignment", null,
+ viewport.alignment.getSequences());
+
+ }
+
protected void cut_actionPerformed()
{
copy_actionPerformed();
protected void delete_actionPerformed()
{
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
- HistoryItem.HIDE));
- if (viewport.getSelectionGroup() == null)
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
{
return;
}
-
- SequenceGroup sg = viewport.getSelectionGroup();
- boolean allSequences = false;
- if(sg.getSize(false)==viewport.alignment.getHeight())
- allSequences = true;
-
- for (int i = 0; i < sg.getSize(false); i++)
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
{
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.getAlignment().findIndex(seq);
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
-
- // If the cut affects all sequences, remove highlighted columns
- if (allSequences)
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.alignment.getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
- if (seq.getSequence().length() < 1)
- {
- viewport.getAlignment().deleteSequence(seq);
- }
- else
- {
- viewport.getAlignment().getSequences().setElementAt(seq, index);
- }
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = (SequenceI) seqs.elementAt(i);
}
+ /*
+ //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand("Cut Sequences",
+ EditCommand.CUT,
+ cut,
+ sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.alignment));
+
viewport.setSelectionGroup(null);
viewport.alignment.deleteGroup(sg);
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+
if (viewport.getAlignment().getHeight() < 1)
{
- try
- {
- this.setVisible(false);
- }
- catch (Exception ex)
- {}
+ this.setVisible(false);
}
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-
}
protected void deleteGroups_actionPerformed()
{
viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
viewport.setSelectionGroup(null);
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
public void selectAllSequenceMenuItem_actionPerformed()
{
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
}
- sg.setEndRes(viewport.alignment.getWidth()-1);
+ sg.setEndRes(viewport.alignment.getWidth() - 1);
viewport.setSelectionGroup(sg);
- alignPanel.repaint();
- PaintRefresher.Refresh(null, viewport.alignment);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void deselectAllSequenceMenuItem_actionPerformed()
{
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
{
- alignPanel.seqPanel.keyboardNo1=null;
- alignPanel.seqPanel.keyboardNo2=null;
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
viewport.setSelectionGroup(null);
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.repaint();
- PaintRefresher.Refresh(null, viewport.alignment);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
public void invertSequenceMenuItem_actionPerformed()
sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
}
- PaintRefresher.Refresh(null, viewport.alignment);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
- public void remove2LeftMenuItem_actionPerformed()
+ void trimAlignment(boolean trimLeft)
{
ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
+
if (colSel.size() > 0)
{
- HistoryItem edit;
- addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,
- HistoryItem.HIDE));
- int min = colSel.getMin();
- viewport.getAlignment().trimLeft(min);
- colSel.compensateForEdit(0, min);
- edit.addShift(0, min);
- if (viewport.getSelectionGroup() != null)
+ if (trimLeft)
{
- viewport.getSelectionGroup().adjustForRemoveLeft(min);
+ column = colSel.getMin();
}
-
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
+ else
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (!sg.adjustForRemoveLeft(min))
- {
- viewport.alignment.deleteGroup(sg);
- }
+ column = colSel.getMax();
}
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
- }
- public void remove2RightMenuItem_actionPerformed()
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- if (colSel.size() > 0)
- {
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
- HistoryItem.HIDE));
- int max = colSel.getMax();
- viewport.getAlignment().trimRight(max);
-
+ SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- viewport.getSelectionGroup().adjustForRemoveRight(max);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ TrimRegionCommand trimRegion;
+ if (trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
+ viewport.setStartRes(0);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT,
+ seqs,
+ column,
+ viewport.alignment,
+ viewport.colSel,
+ viewport.selectionGroup);
}
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
+
+ addHistoryItem(trimRegion);
+
Vector groups = viewport.alignment.getGroups();
+
for (int i = 0; i < groups.size(); i++)
{
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (!sg.adjustForRemoveRight(max))
+
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
{
viewport.alignment.deleteGroup(sg);
}
}
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ }
}
public void removeGappedColumnMenuItem_actionPerformed()
{
- HistoryItem edit;
- addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",
- viewport.alignment,
- HistoryItem.HIDE));
+ int start = 0, end = viewport.alignment.getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
+
+ RemoveGapColCommand removeGapCols =
+ new RemoveGapColCommand("Remove Gapped Columns",
+ seqs,
+ start, end,
+ viewport.alignment);
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
//This is to maintain viewport position on first residue
//of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
- viewport.getAlignment().removeGaps();
-
- viewport.setStartRes(seq.findIndex(startRes)-1);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
}
public void removeAllGapsMenuItem_actionPerformed()
{
- // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences
- // TODO: columnSelection.compensateforedits should be called (and passed to history item)
- HistoryItem editgaps;
- addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,
- HistoryItem.HIDE));
+ int start = 0, end = viewport.alignment.getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
+ hiddenRepSequences);
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.alignment.getSequencesArray();
+ }
//This is to maintain viewport position on first residue
//of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- SequenceI current;
- Vector seqs=null;
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",
+ seqs,
+ start, end,
+ viewport.alignment));
- int start=0, end = viewport.alignment.getWidth();
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
- if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSequences(false) != null
- && viewport.getSelectionGroup().getSize(false)>0)
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+
+ }
+
+ public void findMenuItem_actionPerformed()
+ {
+ new Finder(alignPanel);
+ }
+
+ public void newView()
+ {
+ AlignmentI newal;
+ if (viewport.hasHiddenRows)
{
- seqs = viewport.getSelectionGroup().getSequences(true);
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes()+1;
+ newal = new Alignment(viewport.getAlignment().
+ getHiddenSequences()
+ .getFullAlignment().
+ getSequencesArray());
}
else
- seqs = viewport.alignment.getSequences();
-
- /* Commented out regions below are partial implementation of todo above.
- * divide start,end into visible chunks, and for each:
- int diff=end-start+1;
- int diffmax=0;
- int dr[] = new int[seqs.size()];
- */
- for (int i = 0; i < seqs.size(); i++)
{
- current = (SequenceI) seqs.elementAt(i);
- //dr[i]=
- current.removeGaps(start, end);
- /*if (d<diff) // can only shift
- diff=d;
- if (diffmax<d)
- diffmax=d;
- */
- }
- /* // after the end of each chunk -
- * if (diff>0) {
- // record shift for history.
- editgaps.addShift(start, diff);
- if (viewport.hasHiddenColumns && diffmax>diff) {
- // pad sequence
- StringBuffer gaps=new StringBuffer(diffmax);
- for (int i=0,j=diffmax-diff; i<j; i++)
- gaps.append(viewport.getGapCharacter());
- for (int i=0, j=seqs.size(); i<j; i++) {
- current = (SequenceI) seqs.elementAt(i);
- if (dr[i]-diff>0) {
- String sq = current.getSequence();
- current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
- }
- }
- }
- }*/
-
- viewport.setStartRes(seq.findIndex(startRes)-1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
- }
-
- public void alignmentChanged()
- {
- viewport.alignment.padGaps();
- if(viewport.autocalculateConsensus)
- {
- viewport.updateConsensus();
- viewport.updateConservation();
- }
-
- resetAllColourSchemes();
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
-
- viewport.alignment.adjustSequenceAnnotations();
- alignPanel.repaint();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = viewport.globalColourScheme;
- if(cs!=null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
- resetClustalX(viewport.alignment.getSequences(),
- viewport.alignment.getWidth());
- }
+ newal = new Alignment(viewport.alignment.getSequencesArray());
+ }
- cs.setConsensus(viewport.vconsensus);
- if (cs.conservationApplied())
+ if (viewport.alignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
{
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- cs.setConservation(c);
+ if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+ {
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ }
}
}
- int s, sSize = viewport.alignment.getGroups().size();
- for(s=0; s<sSize; s++)
+ AlignFrame newaf = new AlignFrame(newal,
+ viewport.applet,
+ "",
+ false);
+
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport.
+ getSequenceSetId());
+ int viewSize = -1;
+ for (int i = 0; i < comps.size(); i++)
{
- SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+ if (comps.elementAt(i) instanceof AlignmentPanel)
{
- ((ClustalxColourScheme)sg.cs).resetClustalX(
- sg.getSequences(true), sg.getWidth());
+ viewSize++;
}
- sg.recalcConservation();
}
- }
+ String title = new String(this.getTitle());
+ if (title.indexOf("(View") > -1)
+ {
+ title = title.substring(0, title.indexOf("(View"));
+ }
+ title += "(View " + viewSize + ")";
- public void findMenuItem_actionPerformed()
- {
- new Finder(alignPanel);
- }
+ newaf.setTitle(title.toString());
- public void font_actionPerformed()
- {
- new FontChooser(alignPanel);
- }
+ newaf.viewport.historyList = viewport.historyList;
+ newaf.viewport.redoList = viewport.redoList;
+ }
public void seqLimits_itemStateChanged()
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
-
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
protected void wrapMenuItem_actionPerformed()
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.repaint();
- }
-
-
- protected void scaleAbove_actionPerformed()
- {
- viewport.setScaleAboveWrapped(scaleAbove.getState());
- alignPanel.repaint();
- }
-
- protected void scaleLeft_actionPerformed()
- {
- viewport.setScaleLeftWrapped(scaleLeft.getState());
- alignPanel.repaint();
- }
-
- protected void scaleRight_actionPerformed()
- {
- viewport.setScaleRightWrapped(scaleRight.getState());
- alignPanel.repaint();
- }
-
- public void viewBoxesMenuItem_actionPerformed()
- {
- viewport.setShowBoxes(viewBoxesMenuItem.getState());
- alignPanel.repaint();
- }
-
- public void viewTextMenuItem_actionPerformed()
- {
- viewport.setShowText(viewTextMenuItem.getState());
- alignPanel.repaint();
- }
-
- protected void renderGapsMenuItem_actionPerformed()
- {
- viewport.setRenderGaps(renderGapsMenuItem.getState());
- alignPanel.repaint();
- }
-
- public void annotationPanelMenuItem_actionPerformed()
- {
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
- }
-
- public void featureSettings_actionPerformed()
- {
- new FeatureSettings(viewport, alignPanel);
+ alignPanel.paintAlignment(true);
}
public void overviewMenuItem_actionPerformed()
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.preferredSize().width,
- overview.preferredSize().height + 50);
+ overview.getPreferredSize().width,
+ overview.getPreferredSize().height + 50);
frame.pack();
frame.addWindowListener(new WindowAdapter()
}
- protected void noColourmenuItem_actionPerformed()
- {
- changeColour(null);
- }
-
- public void clustalColour_actionPerformed()
- {
- abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
- viewport.alignment.getWidth()));
- }
-
- public void zappoColour_actionPerformed()
- {
- changeColour(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed()
- {
- changeColour(new TaylorColourScheme());
- }
-
- public void hydrophobicityColour_actionPerformed()
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed()
- {
- changeColour(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed()
- {
- changeColour(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed()
- {
- changeColour(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed()
- {
- changeColour(new BuriedColourScheme());
- }
-
- public void nucleotideColour_actionPerformed()
- {
- changeColour(new NucleotideColourScheme());
- }
-
- protected void applyToAllGroups_actionPerformed()
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
- }
-
void changeColour(ColourSchemeI cs)
{
int threshold = 0;
- if(cs!=null)
+ if (cs != null)
{
if (viewport.getAbovePIDThreshold())
{
cs.setConservation(null);
}
- cs.setConsensus(viewport.vconsensus);
+ cs.setConsensus(viewport.hconsensus);
}
viewport.setGlobalColourScheme(cs);
{
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if(cs==null)
+ if (cs == null)
{
sg.cs = null;
continue;
}
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getWidth());
}
else
{
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
}
else
+ {
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+ }
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3,
- sg.getSequences(true), 0,
+ sg.getSequences(viewport.
+ hiddenRepSequences), 0,
viewport.alignment.getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
}
}
-
if (alignPanel.getOverviewPanel() != null)
{
alignPanel.getOverviewPanel().updateOverviewImage();
}
- alignPanel.repaint();
- }
-
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .sequenceColoursChanged(alignPanel);
+ alignPanel.paintAlignment(true);
+ }
protected void modifyPID_actionPerformed()
{
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)
{
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
"Background");
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
+ if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
{
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
"Background");
modifyPID_actionPerformed();
}
- public void userDefinedColour_actionPerformed()
- {
- new UserDefinedColours(alignPanel, null);
- }
-
- public void PIDColour_actionPerformed()
- {
- changeColour(new PIDColourScheme());
- }
-
- public void BLOSUM62Colour_actionPerformed()
- {
- changeColour(new Blosum62ColourScheme());
- }
-
public void sortPairwiseMenuItem_actionPerformed()
{
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
- HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(),
viewport.getAlignment().getSequenceAt(0));
- alignPanel.repaint();
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
}
public void sortIDMenuItem_actionPerformed()
{
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
- HistoryItem.SORT));
+ // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
+ // HistoryItem.SORT));
AlignmentSorter.sortByID(viewport.getAlignment());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
public void sortGroupMenuItem_actionPerformed()
{
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
- HistoryItem.SORT));
+ // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
+ // HistoryItem.SORT));
AlignmentSorter.sortByGroup(viewport.getAlignment());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
public void removeRedundancyMenuItem_actionPerformed()
{
- new RedundancyPanel(alignPanel);
+ new RedundancyPanel(alignPanel);
}
public void pairwiseAlignmentMenuItem_actionPerformed()
{
- if (viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize(false) > 1)
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 1)
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize(false) < 4 &&
- viewport.getSelectionGroup().getSize(false) > 0)
+ viewport.getSelectionGroup().getSize() < 4 &&
+ viewport.getSelectionGroup().getSize() > 0)
|| viewport.getAlignment().getHeight() < 4)
{
return;
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
void NewTreePanel(String type, String pwType, String title)
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize(false) > 1)
- || (viewport.getSelectionGroup() == null
- && viewport.alignment.getHeight() > 1))
+ viewport.getSelectionGroup().getSize() > 1)
+ || (viewport.getSelectionGroup() == null
+ && viewport.alignment.getHeight() > 1))
{
final TreePanel tp = new TreePanel(viewport,
type,
void loadTree_actionPerformed()
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your Newick tree file here.");
- cap.treeImport = true;
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ cap.setText("Paste your Newick tree file here.");
+ cap.setTreeImport();
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
}
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
public void actionPerformed(ActionEvent evt)
{
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- HistoryItem.SORT));
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.repaint();
+ alignPanel.paintAlignment(true);
}
});
protected void about_actionPerformed()
{
- class AboutPanel extends Canvas
+ class AboutPanel
+ extends Canvas
{
String version;
public AboutPanel(String version)
- { this.version = version; }
+ {
+ this.version = version;
+ }
public void paint(Graphics g)
{
int y = 5, x = 7;
g.setColor(Color.black);
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("Jalview - Release "+version, 200, y += fh);
+ g.drawString("Jalview - Release " + version, 200, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",
x, y += fh * 2);
}
}
-
Frame frame = new Frame();
frame.add(new AboutPanel(version));
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
{
try
{
- System.out.println("Show url: "+url);
+ System.out.println("Show url: " + url);
viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
+ target);
}
catch (Exception ex)
{
}
}
-
//////////////////////////////////////////////////////////////////////////////////
//JBuilder Graphics here
- protected MenuBar alignFrameMenuBar = new MenuBar();
- protected Menu fileMenu = new Menu("File");
- protected MenuItem loadApplication = new MenuItem("View in Full Application");
- protected MenuItem loadTree = new MenuItem("Load Associated Tree");
- protected MenuItem closeMenuItem = new MenuItem("Close");
- protected Menu editMenu = new Menu("Edit");
- protected Menu viewMenu = new Menu("View");
- protected Menu colourMenu = new Menu("Colour");
- protected Menu calculateMenu = new Menu("Calculate");
- protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
- protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
- protected MenuItem remove2LeftMenuItem = new MenuItem();
- protected MenuItem remove2RightMenuItem = new MenuItem();
- protected MenuItem removeGappedColumnMenuItem = new MenuItem();
- protected MenuItem removeAllGapsMenuItem = new MenuItem();
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
- protected MenuItem sortPairwiseMenuItem = new MenuItem();
- protected MenuItem sortIDMenuItem = new MenuItem();
- protected MenuItem sortGroupMenuItem = new MenuItem();
- protected MenuItem removeRedundancyMenuItem = new MenuItem();
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();
- protected MenuItem PCAMenuItem = new MenuItem();
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();
- protected MenuItem neighbourTreeMenuItem = new MenuItem();
- BorderLayout borderLayout1 = new BorderLayout();
- public Label statusBar = new Label();
- protected Menu outputTextboxMenu = new Menu();
- protected MenuItem clustalColour = new MenuItem();
- protected MenuItem zappoColour = new MenuItem();
- protected MenuItem taylorColour = new MenuItem();
- protected MenuItem hydrophobicityColour = new MenuItem();
- protected MenuItem helixColour = new MenuItem();
- protected MenuItem strandColour = new MenuItem();
- protected MenuItem turnColour = new MenuItem();
- protected MenuItem buriedColour = new MenuItem();
- protected MenuItem userDefinedColour = new MenuItem();
- protected MenuItem PIDColour = new MenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
- MenuItem njTreeBlosumMenuItem = new MenuItem();
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
- MenuItem overviewMenuItem = new MenuItem();
- protected MenuItem undoMenuItem = new MenuItem();
- protected MenuItem redoMenuItem = new MenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
- MenuItem noColourmenuItem = new MenuItem();
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
- MenuItem findMenuItem = new MenuItem();
- Menu searchMenu = new Menu();
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
- protected MenuItem nucleotideColour = new MenuItem();
- MenuItem deleteGroups = new MenuItem();
- MenuItem delete = new MenuItem();
- MenuItem copy = new MenuItem();
- MenuItem cut = new MenuItem();
- Menu pasteMenu = new Menu();
- MenuItem pasteNew = new MenuItem();
- MenuItem pasteThis = new MenuItem();
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
- protected MenuItem font = new MenuItem();
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();
- MenuItem modifyPID = new MenuItem();
- MenuItem modifyConservation = new MenuItem();
- protected CheckboxMenuItem autoCalculate
- = new CheckboxMenuItem("Autocalculate Consensus", true);
- protected Menu sortByTreeMenu = new Menu();
- Menu sort = new Menu();
- Menu calculate = new Menu();
- MenuItem inputText = new MenuItem();
- Menu helpMenu = new Menu();
- MenuItem documentation = new MenuItem();
- MenuItem about = new MenuItem();
- protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+ MenuBar alignFrameMenuBar = new MenuBar();
+ Menu fileMenu = new Menu("File");
+ MenuItem loadApplication = new MenuItem("View in Full Application");
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");
+ MenuItem loadAnnotations = new MenuItem(
+ "Load Features/Annotations ...");
+ MenuItem outputFeatures = new MenuItem("Export Features ...");
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
+
+ MenuItem closeMenuItem = new MenuItem("Close");
+ Menu editMenu = new Menu("Edit");
+ Menu viewMenu = new Menu("View");
+ Menu colourMenu = new Menu("Colour");
+ Menu calculateMenu = new Menu("Calculate");
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
+ MenuItem remove2LeftMenuItem = new MenuItem();
+ MenuItem remove2RightMenuItem = new MenuItem();
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+ MenuItem sortIDMenuItem = new MenuItem();
+ MenuItem sortGroupMenuItem = new MenuItem();
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+ MenuItem PCAMenuItem = new MenuItem();
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
+ MenuItem neighbourTreeMenuItem = new MenuItem();
+ BorderLayout borderLayout1 = new BorderLayout();
+ public Label statusBar = new Label();
+ Menu outputTextboxMenu = new Menu();
+ MenuItem clustalColour = new MenuItem();
+ MenuItem zappoColour = new MenuItem();
+ MenuItem taylorColour = new MenuItem();
+ MenuItem hydrophobicityColour = new MenuItem();
+ MenuItem helixColour = new MenuItem();
+ MenuItem strandColour = new MenuItem();
+ MenuItem turnColour = new MenuItem();
+ MenuItem buriedColour = new MenuItem();
+ MenuItem userDefinedColour = new MenuItem();
+ MenuItem PIDColour = new MenuItem();
+ MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem njTreeBlosumMenuItem = new MenuItem();
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+ MenuItem alProperties = new MenuItem("Alignment Properties...");
+ MenuItem overviewMenuItem = new MenuItem();
+ MenuItem undoMenuItem = new MenuItem();
+ MenuItem redoMenuItem = new MenuItem();
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ MenuItem noColourmenuItem = new MenuItem();
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+ MenuItem findMenuItem = new MenuItem();
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+ MenuItem nucleotideColour = new MenuItem();
+ MenuItem deleteGroups = new MenuItem();
+ MenuItem delete = new MenuItem();
+ MenuItem copy = new MenuItem();
+ MenuItem cut = new MenuItem();
+ Menu pasteMenu = new Menu();
+ MenuItem pasteNew = new MenuItem();
+ MenuItem pasteThis = new MenuItem();
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+ MenuItem font = new MenuItem();
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+ MenuItem modifyPID = new MenuItem();
+ MenuItem modifyConservation = new MenuItem();
+ CheckboxMenuItem autoCalculate
+ = new CheckboxMenuItem("Autocalculate Consensus", true);
+ Menu sortByTreeMenu = new Menu();
+ Menu sort = new Menu();
+ Menu calculate = new Menu();
+ MenuItem inputText = new MenuItem();
+ Menu helpMenu = new Menu();
+ MenuItem documentation = new MenuItem();
+ MenuItem about = new MenuItem();
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
Panel embeddedMenu;
Label embeddedEdit;
- Label embeddedSearch;
+ Label embeddedSelect;
Label embeddedView;
+ Label embeddedFormat;
Label embeddedColour;
Label embeddedFile;
Label embeddedHelp;
Label embeddedCalculate;
FlowLayout flowLayout1;
- private void jbInit() throws Exception {
+ private void jbInit()
+ throws Exception
+ {
- setMenuBar(alignFrameMenuBar);
+ setMenuBar(alignFrameMenuBar);
- MenuItem item;
+ MenuItem item;
- // dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
+ // dynamically fill save as menu with available formats
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
+ i++)
+ {
- item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
{
- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
-
- outputTextboxMenu.add(item);
- }
- closeMenuItem.addActionListener(this);
- loadApplication.addActionListener(this);
-
- loadTree.addActionListener(this);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(
- "Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(this);
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
-
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(
- "Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- searchMenu.setLabel("Search");
-
- abovePIDThreshold.setLabel("Above Identity Threshold");
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
- modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
- autoCalculate.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
-
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
-
- about.setLabel("About...");
- about.addActionListener(this);
- seqLimits.setState(true);
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add(item);
+ }
+ closeMenuItem.addActionListener(this);
+ loadApplication.addActionListener(this);
+
+ loadTree.addActionListener(this);
+ loadAnnotations.addActionListener(this);
+ outputFeatures.addActionListener(this);
+ outputAnnotations.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.addActionListener(this);
+ remove2LeftMenuItem.setLabel("Remove Left");
+ remove2LeftMenuItem.addActionListener(this);
+ remove2RightMenuItem.setLabel("Remove Right");
+ remove2RightMenuItem.addActionListener(this);
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
+ removeGappedColumnMenuItem.addActionListener(this);
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");
+ removeAllGapsMenuItem.addActionListener(this);
+ viewBoxesMenuItem.setLabel("Boxes");
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addItemListener(this);
+ viewTextMenuItem.setLabel("Text");
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addItemListener(this);
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel("by ID");
+ sortIDMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel("by Group");
+ sortGroupMenuItem.addActionListener(this);
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");
+ removeRedundancyMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel("Principal Component Analysis");
+ PCAMenuItem.addActionListener(this);
+ averageDistanceTreeMenuItem.setLabel(
+ "Average Distance Using % Identity");
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
+ neighbourTreeMenuItem.addActionListener(this);
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setText("Status bar");
+ outputTextboxMenu.setLabel("Output to Textbox");
+ clustalColour.setLabel("Clustalx");
+
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel("Zappo");
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel("Taylor");
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.addActionListener(this);
+ helixColour.setLabel("Helix Propensity");
+ helixColour.addActionListener(this);
+ strandColour.setLabel("Strand Propensity");
+ strandColour.addActionListener(this);
+ turnColour.setLabel("Turn Propensity");
+ turnColour.addActionListener(this);
+ buriedColour.setLabel("Buried Index");
+ buriedColour.addActionListener(this);
+ userDefinedColour.setLabel("User Defined...");
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel("Percentage Identity");
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");
+ BLOSUM62Colour.addActionListener(this);
+ avDistanceTreeBlosumMenuItem.setLabel(
+ "Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
+ njTreeBlosumMenuItem.addActionListener(this);
+ annotationPanelMenuItem.setLabel("Show Annotations");
+ annotationPanelMenuItem.addItemListener(this);
+ colourTextMenuItem.setLabel("Colour Text");
+ colourTextMenuItem.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel("Overview Window");
+ overviewMenuItem.addActionListener(this);
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel("Undo");
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel("Redo");
+ redoMenuItem.addActionListener(this);
+ conservationMenuItem.setLabel("by Conservation");
+ conservationMenuItem.addItemListener(this);
+ noColourmenuItem.setLabel("None");
+ noColourmenuItem.addActionListener(this);
+ wrapMenuItem.setLabel("Wrap");
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel("Show Gaps");
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ findMenuItem.setLabel("Find...");
+ findMenuItem.addActionListener(this);
+ abovePIDThreshold.setLabel("Above Identity Threshold");
+ abovePIDThreshold.addItemListener(this);
+ nucleotideColour.setLabel("Nucleotide");
+ nucleotideColour.addActionListener(this);
+ deleteGroups.setLabel("Undefine Groups");
+ deleteGroups.addActionListener(this);
+ copy.setLabel("Copy");
+ copy.addActionListener(this);
+ cut.setLabel("Cut");
+ cut.addActionListener(this);
+ delete.setLabel("Delete");
+ delete.addActionListener(this);
+ pasteMenu.setLabel("Paste");
+ pasteNew.setLabel("To New Alignment");
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel("Add To This Alignment");
+ pasteThis.addActionListener(this);
+ applyToAllGroups.setLabel("Apply Colour To All Groups");
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ font.setLabel("Font...");
+ font.addActionListener(this);
+ scaleAbove.setLabel("Scale Above");
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel("Scale Left");
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel("Scale Right");
+ scaleRight.addItemListener(this);
+ modifyPID.setLabel("Modify Identity Threshold...");
+ modifyPID.addActionListener(this);
+ modifyConservation.setLabel("Modify Conservation Threshold...");
+ modifyConservation.addActionListener(this);
+ sortByTreeMenu.setLabel("By Tree Order");
+ sort.setLabel("Sort");
+ calculate.setLabel("Calculate Tree");
+ autoCalculate.addItemListener(this);
+ inputText.setLabel("Input from textbox");
+ inputText.addActionListener(this);
+
+ helpMenu.setLabel("Help");
+ documentation.setLabel("Documentation");
+ documentation.addActionListener(this);
+
+ about.setLabel("About...");
+ about.addActionListener(this);
+ seqLimits.setState(true);
seqLimits.setLabel("Show Sequence Limits");
seqLimits.addItemListener(this);
featureSettings.setLabel("Feature Settings...");
showSeqs.addActionListener(this);
hideColumns.addActionListener(this);
hideSequences.addActionListener(this);
-
-
+ formatMenu.setLabel("Format");
+ selectMenu.setLabel("Select");
+ newView.setLabel("New View");
+ newView.addActionListener(this);
alignFrameMenuBar.add(fileMenu);
- alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
- alignFrameMenuBar.add(viewMenu);
- alignFrameMenuBar.add(colourMenu);
- alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(helpMenu);
- fileMenu.add(inputText);
- fileMenu.add(outputTextboxMenu);
- if(jalviewServletURL!=null)
- fileMenu.add(loadApplication);
- fileMenu.addSeparator();
- fileMenu.add(loadTree);
- fileMenu.add(closeMenuItem);
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.add(cut);
- editMenu.add(copy);
- editMenu.add(pasteMenu);
- editMenu.add(delete);
- editMenu.addSeparator();
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(invertColSel);
- editMenu.add(deleteGroups);
- editMenu.addSeparator();
- editMenu.add(remove2LeftMenuItem);
- editMenu.add(remove2RightMenuItem);
- editMenu.add(removeGappedColumnMenuItem);
- editMenu.add(removeAllGapsMenuItem);
- editMenu.add(removeRedundancyMenuItem);
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.addSeparator();
+ alignFrameMenuBar.add(editMenu);
+ alignFrameMenuBar.add(selectMenu);
+ alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(formatMenu);
+ alignFrameMenuBar.add(colourMenu);
+ alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(helpMenu);
+
+ fileMenu.add(inputText);
+ fileMenu.add(loadTree);
+ fileMenu.add(loadAnnotations);
+
+ fileMenu.addSeparator();
+ fileMenu.add(outputTextboxMenu);
+ fileMenu.add(outputFeatures);
+ fileMenu.add(outputAnnotations);
+
+ if (jalviewServletURL != null)
+ {
+ fileMenu.add(loadApplication);
+ }
+
+ fileMenu.addSeparator();
+ fileMenu.add(closeMenuItem);
+
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
+ editMenu.addSeparator();
+ editMenu.add(remove2LeftMenuItem);
+ editMenu.add(remove2RightMenuItem);
+ editMenu.add(removeGappedColumnMenuItem);
+ editMenu.add(removeAllGapsMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ viewMenu.add(newView);
+ viewMenu.addSeparator();
viewMenu.add(menu1);
viewMenu.add(menu2);
viewMenu.addSeparator();
- viewMenu.add(wrapMenuItem);
- viewMenu.add(scaleAbove);
- viewMenu.add(scaleLeft);
- viewMenu.add(scaleRight);
- viewMenu.addSeparator();
- viewMenu.add(seqLimits);
- viewMenu.add(viewBoxesMenuItem);
- viewMenu.add(viewTextMenuItem);
- viewMenu.add(colourTextMenuItem);
- viewMenu.add(renderGapsMenuItem);
- viewMenu.add(annotationPanelMenuItem);
+ viewMenu.add(annotationPanelMenuItem);
viewMenu.addSeparator();
- viewMenu.add(sequenceFeatures);
- viewMenu.add(featureSettings);
+ viewMenu.add(sequenceFeatures);
+ viewMenu.add(featureSettings);
viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
+ viewMenu.add(alProperties);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
+ colourMenu.add(applyToAllGroups);
+ colourMenu.addSeparator();
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
calculateMenu.add(sort);
- calculateMenu.add(calculate);
- calculateMenu.addSeparator();
- calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
- calculateMenu.add(autoCalculate);
- this.add(statusBar, BorderLayout.SOUTH);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- helpMenu.add(documentation);
- helpMenu.add(about);
+ calculateMenu.add(calculate);
+ calculateMenu.addSeparator();
+ calculateMenu.add(pairwiseAlignmentMenuItem);
+ calculateMenu.add(PCAMenuItem);
+ calculateMenu.add(autoCalculate);
+ this.add(statusBar, BorderLayout.SOUTH);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
+ sort.add(sortIDMenuItem);
+ sort.add(sortByTreeMenu);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ calculate.add(averageDistanceTreeMenuItem);
+ calculate.add(neighbourTreeMenuItem);
+ calculate.add(avDistanceTreeBlosumMenuItem);
+ calculate.add(njTreeBlosumMenuItem);
+ helpMenu.add(documentation);
+ helpMenu.add(about);
menu1.add(showColumns);
menu1.add(showSeqs);
menu2.add(hideColumns);
menu2.add(hideSequences);
+ formatMenu.add(font);
+ formatMenu.add(seqLimits);
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(deleteGroups);
}
public void setEmbedded()
{
embeddedMenu = new Panel();
- embeddedEdit = new Label();
- embeddedSearch = new Label();
- embeddedView = new Label();
- embeddedColour = new Label();
- embeddedFile = new Label();
- embeddedHelp = new Label();
- embeddedCalculate = new Label();
+ embeddedEdit = new Label("Edit");
+ embeddedSelect = new Label("Select");
+ embeddedView = new Label("View");
+ embeddedFormat = new Label("Format");
+ embeddedColour = new Label("Colour");
+ embeddedFile = new Label("File");
+ embeddedHelp = new Label("Help");
+ embeddedCalculate = new Label("Calculate");
flowLayout1 = new FlowLayout();
embeddedMenu.setBackground(Color.lightGray);
embeddedMenu.setLayout(flowLayout1);
- embeddedEdit.setText("Edit");
embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedSearch.setText("Search");
- embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedView.setText("View");
+ embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedColour.setText("Colour");
+ embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedFile.setText("File");
embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedHelp.setText("Help");
embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));
- embeddedCalculate.setText("Calculate");
embeddedMenu.add(embeddedFile);
embeddedMenu.add(embeddedEdit);
- embeddedMenu.add(embeddedSearch);
+ embeddedMenu.add(embeddedSelect);
embeddedMenu.add(embeddedView);
+ embeddedMenu.add(embeddedFormat);
embeddedMenu.add(embeddedColour);
embeddedMenu.add(embeddedCalculate);
embeddedMenu.add(embeddedHelp);
flowLayout1.setVgap(0);
embeddedFile.addMouseListener(this);
embeddedEdit.addMouseListener(this);
- embeddedSearch.addMouseListener(this);
+ embeddedSelect.addMouseListener(this);
embeddedView.addMouseListener(this);
+ embeddedFormat.addMouseListener(this);
embeddedColour.addMouseListener(this);
embeddedCalculate.addMouseListener(this);
embeddedHelp.addMouseListener(this);
- // setVisible(false);
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Seperator
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
viewport.applet.add(statusBar, BorderLayout.SOUTH);
- // viewport.applet.validate();
- alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
+ alignPanel.setSize(viewport.applet.getSize().width,
+ viewport.applet.getSize().height
- embeddedMenu.HEIGHT - statusBar.HEIGHT);
- viewport.applet.add(alignPanel, BorderLayout.CENTER);
- viewport.applet.validate();
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);
+ viewport.applet.validate();
}
-
-
PopupMenu filePopup, editPopup, searchPopup,
- viewPopup, colourPopup, calculatePopup, helpPopup;
+ viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
MenuItem annotationColour = new MenuItem();
Menu menu2 = new Menu();
MenuItem hideColumns = new MenuItem();
MenuItem hideSequences = new MenuItem();
+ Menu formatMenu = new Menu();
+ Menu selectMenu = new Menu();
+ MenuItem newView = new MenuItem();
public void mousePressed(MouseEvent evt)
{
PopupMenu popup = null;
- Label source = (Label)evt.getSource();
- if(source==embeddedFile)
+ Label source = (Label) evt.getSource();
+ if (source == embeddedFile)
{
popup = filePopup = genPopupMenu(filePopup, fileMenu);
}
- else if(source==embeddedEdit)
+ else if (source == embeddedEdit)
{
popup = editPopup = genPopupMenu(editPopup, editMenu);
}
- else if(source==embeddedSearch)
+ else if (source == embeddedSelect)
{
- popup = searchPopup = genPopupMenu(searchPopup, searchMenu);
+ popup = searchPopup = genPopupMenu(searchPopup, selectMenu);
}
- else if(source==embeddedView)
+ else if (source == embeddedView)
{
popup = viewPopup = genPopupMenu(viewPopup, viewMenu);
}
- else if(source==embeddedColour)
+ else if (source == embeddedFormat)
+ {
+ popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
+ }
+ else if (source == embeddedColour)
{
popup = colourPopup = genPopupMenu(colourPopup, colourMenu);
}
- else if(source==embeddedCalculate)
+ else if (source == embeddedCalculate)
{
popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);
}
- else if(source==embeddedHelp)
+ else if (source == embeddedHelp)
{
popup = helpPopup = genPopupMenu(helpPopup, helpMenu);
}
PopupMenu genPopupMenu(PopupMenu popup, Menu original)
{
- if(popup!=null)
+ if (popup != null)
{
return popup;
}
popup = new PopupMenu();
int m, mSize = original.getItemCount();
- for(m=0; m<mSize; m++)
+ for (m = 0; m < mSize; m++)
{
popup.add(original.getItem(m));
mSize--;
return popup;
}
+
public void mouseClicked(MouseEvent evt)
{}
+
public void mouseReleased(MouseEvent evt)
{}
+
public void mouseEntered(MouseEvent evt)
{}
+
public void mouseExited(MouseEvent evt)
{}
}
-
git://source.jalview.org / jalview.git / blobdiff