import jalview.io.*;
import jalview.schemes.*;
-public class AlignFrame
- extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+ ItemListener, KeyListener
{
public AlignmentPanel alignPanel;
+
public AlignViewport viewport;
+
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)
{
if (applet != null)
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
int height = Integer.parseInt(param);
DEFAULT_HEIGHT = height;
}
+ } catch (Exception ex)
+ {
}
- 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
+ // 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);
/**
* DOCUMENT ME!
- *
- * @param String DOCUMENT ME!
+ *
+ * @param String
+ * DOCUMENT ME!
*/
public void parseFeaturesFile(String file, String type)
boolean featuresFile = false;
try
{
- featuresFile = new jalview.io.FeaturesFile(file,
- type).parse(viewport.alignment,
- alignPanel.seqPanel.seqCanvas.
- getFeatureRenderer().featureColours,
- featureLinks,
- true);
- }
- catch (Exception ex)
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(
+ viewport.alignment, alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().featureColours, featureLinks,
+ true);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
{
if (featureLinks.size() > 0)
{
- alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureLinks = featureLinks;
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
}
viewport.showSequenceFeatures = true;
sequenceFeatures.setState(true);
public void keyPressed(KeyEvent evt)
{
- 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());
-
+ 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())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed();
- break;
- case KeyEvent.VK_X:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- cut_actionPerformed();
- }
- break;
- case KeyEvent.VK_C:
- if (viewport.cursorMode && !evt.isControlDown())
- {
- alignPanel.seqPanel.setCursorColumn();
- }
- if (evt.isControlDown() || evt.isMetaDown())
- {
- copy_actionPerformed();
- }
- break;
- case KeyEvent.VK_V:
- if (evt.isControlDown())
- {
- paste(evt.isShiftDown());
- }
- break;
- case KeyEvent.VK_A:
- if (evt.isControlDown() || evt.isMetaDown())
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- break;
- case KeyEvent.VK_DOWN:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, 1);
- }
- else
- {
- moveSelectedSequences(false);
- }
- break;
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed();
+ break;
+ case KeyEvent.VK_X:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ cut_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ copy_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_V:
+ if (evt.isControlDown())
+ {
+ paste(evt.isShiftDown());
+ }
+ break;
+ case KeyEvent.VK_A:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ {
+ moveSelectedSequences(false);
+ }
+ break;
- case KeyEvent.VK_UP:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.moveCursor(0, -1);
- }
- else
- {
- moveSelectedSequences(true);
- }
- break;
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ {
+ moveSelectedSequences(true);
+ }
+ break;
- case KeyEvent.VK_LEFT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(false,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( -1, 0);
- break;
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(-1, 0);
+ break;
- case KeyEvent.VK_RIGHT:
- if (evt.isAltDown() || !viewport.cursorMode)
- slideSequences(true,
- alignPanel.seqPanel.getKeyboardNo1());
- else
- alignPanel.seqPanel.moveCursor( 1, 0);
- break;
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ else
+ alignPanel.seqPanel.moveCursor(1, 0);
+ break;
- case KeyEvent.VK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown()
- );
- }
- break;
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
- case KeyEvent.VK_DELETE:
- case KeyEvent.VK_BACK_SPACE:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
- || evt.isShiftDown()
- || evt.isAltDown());
- }
- else
- {
- cut_actionPerformed();
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- break;
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ else
+ {
+ cut_actionPerformed();
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ break;
- case KeyEvent.VK_S:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRow();
- }
- break;
- case KeyEvent.VK_P:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorPosition();
- }
- break;
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
- case KeyEvent.VK_ENTER:
- case KeyEvent.VK_COMMA:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setCursorRowAndColumn();
- }
- break;
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
- case KeyEvent.VK_Q:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);
- }
- break;
- case KeyEvent.VK_M:
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);
- }
- break;
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ 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;
+ }
+ break;
+
+ case KeyEvent.VK_F:
+ if (evt.isControlDown())
+ {
+ findMenuItem_actionPerformed();
+ }
+ break;
- case KeyEvent.VK_F2:
- viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText("Keyboard editing mode is " +
- (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
{
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ hide = true;
+ viewport.hideAllSelectedSeqs();
}
- break;
-
- case KeyEvent.VK_F:
- if (evt.isControlDown())
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
{
- findMenuItem_actionPerformed();
+ viewport.showAllHiddenSeqs();
}
- break;
+ }
- case KeyEvent.VK_H:
+ if (toggleCols)
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
-
- if (toggleSeqs)
+ if (viewport.colSel.getSelected().size() > 0)
{
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ viewport.hideSelectedColumns();
+ if (!toggleSeqs)
{
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- viewport.showAllHiddenSeqs();
+ viewport.selectionGroup = sg;
}
}
-
- if (toggleCols)
+ else if (!hide)
{
- if (viewport.colSel.getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
+ viewport.showAllHiddenColumns();
}
- break;
}
+ 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_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_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_Z:
+ if (evt.isControlDown())
+ {
+ undoMenuItem_actionPerformed();
+ }
+ break;
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_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_L:
+ if (evt.isControlDown())
+ {
+ trimAlignment(true);
+ }
+ break;
- case KeyEvent.VK_R:
- if (evt.isControlDown())
- {
- trimAlignment(false);
- }
- break;
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
- case KeyEvent.VK_E:
- if (evt.isControlDown())
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
{
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
+ this.removeAllGapsMenuItem_actionPerformed();
}
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
+ else
{
- if (evt.isAltDown())
- {
- viewport.invertColumnSelection();
- }
- else
- {
- this.invertSequenceMenuItem_actionPerformed();
- }
+ removeGappedColumnMenuItem_actionPerformed();
}
- break;
-
- case KeyEvent.VK_U:
- if (evt.isControlDown())
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
{
- this.deleteGroups_actionPerformed();
+ viewport.invertColumnSelection();
}
- break;
-
- case KeyEvent.VK_T:
- if (evt.isControlDown())
+ else
{
- newView(null);
+ this.invertSequenceMenuItem_actionPerformed();
}
- break;
+ }
+ break;
+
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
}
alignPanel.paintAlignment(true);
}
public void keyReleased(KeyEvent evt)
- {}
+ {
+ }
public void keyTyped(KeyEvent evt)
- {}
+ {
+ }
public void itemStateChanged(ItemEvent evt)
{
else if (evt.getSource() == autoCalculate)
{
viewport.autocalculateConsensus = autoCalculate.getState();
- } else if (evt.getSource() == this.centreColumnLabelFlag)
+ }
+ else if (evt.getSource() == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
}
-
+
alignPanel.paintAlignment(true);
}
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- else if (source == hideSequences && viewport.getSelectionGroup() != null)
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
}
{
new FeatureSettings(alignPanel);
}
- else if(source== alProperties)
+ else if (source == alProperties)
{
- StringBuffer contents = new StringBuffer();
+ 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();
+ 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);
+ 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)
+ if (((Alignment) viewport.alignment).alignmentProperties != null)
+ {
+ Hashtable props = ((Alignment) viewport.alignment).alignmentProperties;
+ Enumeration en = props.keys();
+ while (en.hasMoreElements())
{
- 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));
- }
+ 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);
+ 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)
{
else if (source == clustalColour)
{
abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
- viewport.alignment.getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.alignment
+ .getSequences(), viewport.alignment.getWidth()));
}
else if (source == zappoColour)
{
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(),
- viewport.showJVSuffix));
+ jalview.bin.JalviewLite.addFrame(frame, "Alignment output - "
+ + e.getActionCommand(), 600, 500);
+ cap.setText(new AppletFormatAdapter().formatSequences(e
+ .getActionCommand(), viewport.getAlignment(),
+ viewport.showJVSuffix));
}
public void loadAnnotations()
public String outputAnnotations(boolean displayTextbox)
{
String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
- viewport.alignment.getGroups(),
- ((Alignment) viewport.alignment).alignmentProperties);
+ 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);
+ jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
cap.setText(annotation);
}
String features;
if (format.equalsIgnoreCase("Jalview"))
{
- features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ features = new FeaturesFile().printJalviewFormat(viewport.alignment
+ .getSequencesArray(), viewport.featuresDisplayed);
}
else
{
- features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ 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);
+ jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
cap.setText(features);
}
{
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)
{
if (viewport.applet.getParameter("annotations") != null)
{
url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+ url
+ .append(appendProtocol(viewport.applet
+ .getParameter("annotations")));
}
if (viewport.applet.getParameter("jnetfile") != null)
if (viewport.applet.getParameter("defaultColour") != null)
{
- url.append("&colour=" +
- removeWhiteSpace(viewport.applet.getParameter("defaultColour"))
- );
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("defaultColour")));
}
if (viewport.applet.getParameter("userDefinedColour") != null)
{
- url.append("&colour=" +
- removeWhiteSpace(viewport.applet.getParameter(
- "userDefinedColour"))
- );
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("userDefinedColour")));
}
- if (viewport.applet.getParameter("tree")!=null)
+ if (viewport.applet.getParameter("tree") != null)
{
- url.append("&tree="+appendProtocol(viewport.applet.getParameter("tree")));
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("tree")));
}
- if (viewport.applet.getParameter("treeFile")!=null)
+ if (viewport.applet.getParameter("treeFile") != null)
{
- url.append("&tree="+appendProtocol(viewport.applet.getParameter("treeFile")));
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("treeFile")));
}
showURL(url.toString(), "FULL_APP");
new URL(url);
url = URLEncoder.encode(url);
}
- /* When we finally deprecate 1.1 compatibility,
- * we can start to use URLEncoder.encode(url,"UTF-8")
- * and then we'll need this catch:
- * catch (UnsupportedEncodingException ex)
- {
- System.err.println("WARNING - IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
- ex.printStackTrace();
- } */
+ /*
+ * When we finally deprecate 1.1 compatibility, we can start to use
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
+ * ex.printStackTrace(); }
+ */
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
}
}
+
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void undoMenuItem_actionPerformed()
{
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
updateEditMenuBar();
originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.alignment.getSequences());
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void redoMenuItem_actionPerformed()
{
updateEditMenuBar();
originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
+ originalSource.alignment.getSequences());
}
AlignViewport getOriginatingSource(CommandI command)
{
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
+ // 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());
+ 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)
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
{
- originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+ 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
+ // The original view is closed, we must validate
+ // the current view against the closed view first
if (al != null)
{
PaintRefresher.validateSequences(al, viewport.alignment);
synchronized void slideSequences(boolean right, int size)
{
Vector sg = new Vector();
- if(viewport.cursorMode)
+ if (viewport.cursorMode)
+ {
+ sg.addElement(viewport.alignment
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport.alignment
+ .getHeight())
{
- sg.addElement(viewport.alignment.getSequenceAt(
- alignPanel.seqPanel.seqCanvas.cursorY));
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.hiddenRepSequences);
}
- else if(viewport.getSelectionGroup()!=null
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
- if(sg.size()<1)
+ if (sg.size() < 1)
{
return;
}
for (int i = 0; i < viewport.alignment.getHeight(); i++)
{
- if(!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+ if (!sg.contains(viewport.alignment.getSequenceAt(i)))
+ invertGroup.addElement(viewport.alignment.getSequenceAt(i));
}
SequenceI[] seqs1 = new SequenceI[sg.size()];
SlideSequencesCommand ssc;
if (right)
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs2, seqs1, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
+ size, viewport.getGapCharacter());
else
- ssc = new SlideSequencesCommand("Slide Sequences",
- seqs1, seqs2, size,
- viewport.getGapCharacter()
- );
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
+ size, viewport.getGapCharacter());
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor( -size, 0);
+ alignPanel.seqPanel.moveCursor(-size, 0);
else
groupAdjustment = -size;
}
if (groupAdjustment != 0)
{
viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);
viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);
}
-
boolean appendHistoryItem = false;
- if(viewport.historyList!=null
- && viewport.historyList.size()>0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
+ if (viewport.historyList != null && viewport.historyList.size() > 0
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)
{
- appendHistoryItem = ssc.appendSlideCommand(
- (SlideSequencesCommand)viewport.historyList.peek())
- ;
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+ .peek());
}
- if(!appendHistoryItem)
+ if (!appendHistoryItem)
addHistoryItem(ssc);
repaint();
}
static StringBuffer copiedSequences;
+
static Vector copiedHiddenColumns;
+
protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();
- i++)
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
+ .size(); i++)
{
- int[] region = (int[])
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);
+ int[] region = (int[]) viewport.getColumnSelection()
+ .getHiddenColumns().elementAt(i);
copiedHiddenColumns.addElement(new int[]
- {region[0] - hiddenOffset,
- region[1] - hiddenOffset});
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
}
}
else
}
}
- //FIND START RES
- //Returns residue following index if gap
+ // 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
+ // 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)))
+ if (!jalview.util.Comparison.isGap((ch)))
{
endRes++;
}
endRes += seq.getStart() - 1;
}
- copiedSequences.append(seq.getName() + "\t" +
- startRes + "\t" +
- endRes + "\t" +
- seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
+ copiedSequences.append(seq.getName()
+ + "\t"
+ + startRes
+ + "\t"
+ + endRes
+ + "\t"
+ + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
}
}
newtitle = newtitle.concat("- from " + getTitle());
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet,
- newtitle,
- false);
+ viewport.applet, newtitle, false);
if (copiedHiddenColumns != null)
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
}
jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ DEFAULT_HEIGHT);
}
else
{
addSequences(newSeqs);
}
- }
- catch (Exception ex)
- {} // could be anything being pasted in here
+ } catch (Exception ex)
+ {
+ } // could be anything being pasted in here
}
viewport.alignment.addSequence(seqs[i]);
}
- //!newAlignment
- addHistoryItem(new EditCommand(
- "Add sequences",
- EditCommand.PASTE,
- seqs,
- 0,
- viewport.alignment.getWidth(),
- viewport.alignment)
- );
+ // !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());
+ viewport.firePropertyChange("alignment", null, viewport.alignment
+ .getSequences());
}
if (sg.getSize() == viewport.alignment.getHeight())
{
viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
+ sg.getEndRes() + 1);
}
SequenceI[] cut = new SequenceI[seqs.size()];
}
/*
- //ADD HISTORY ITEM
+ * //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences",
- EditCommand.CUT,
- cut,
- sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
+ 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.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
if (viewport.getAlignment().getHeight() < 1)
{
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
}
else
{
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT,
- seqs,
- column,
- viewport.alignment,
- viewport.colSel,
- viewport.selectionGroup);
+ 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);
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.alignment, viewport.colSel,
+ viewport.selectionGroup);
}
statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
{
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if ( (trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ 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());
}
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
seqs = viewport.alignment.getSequencesArray();
}
- RemoveGapColCommand removeGapCols =
- new RemoveGapColCommand("Remove Gapped Columns",
- seqs,
- start, end,
- viewport.alignment);
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end, viewport.alignment);
addHistoryItem(removeGapCols);
- statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");
+ statusBar.setText("Removed " + removeGapCols.getSize()
+ + " empty columns.");
- //This is to maintain viewport position on first residue
- //of first sequence
+ // 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.getColumnSelection().compensateForEdits(shifts);
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
SequenceI[] seqs;
if (viewport.getSelectionGroup() != null)
{
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.
- hiddenRepSequences);
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.hiddenRepSequences);
start = viewport.getSelectionGroup().getStartRes();
end = viewport.getSelectionGroup().getEndRes();
}
seqs = viewport.alignment.getSequencesArray();
}
- //This is to maintain viewport position on first residue
- //of first sequence
+ // This is to maintain viewport position on first residue
+ // of first sequence
SequenceI seq = viewport.alignment.getSequenceAt(0);
int startRes = seq.findPosition(viewport.startRes);
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",
- seqs,
- start, end,
- viewport.alignment));
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.alignment));
viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
}
{
new Finder(alignPanel);
}
+
/**
* create a new view derived from the current view
+ *
* @param viewtitle
* @return frame for the new view
*/
AlignmentI newal;
if (viewport.hasHiddenRows)
{
- newal = new Alignment(viewport.getAlignment().
- getHiddenSequences()
- .getFullAlignment().
- getSequencesArray());
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()
+ .getFullAlignment().getSequencesArray());
}
else
{
{
if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
{
- newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+ newal
+ .addAnnotation(viewport.alignment
+ .getAlignmentAnnotation()[i]);
}
}
}
- AlignFrame newaf = new AlignFrame(newal,
- viewport.applet,
- "",
- false);
+ 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, newaf.alignPanel.av
+ .getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
- newaf.alignPanel.av.getSequenceSetId());
+ newaf.alignPanel.av.getSequenceSetId());
- Vector comps = (Vector) PaintRefresher.components.get(viewport.
- getSequenceSetId());
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
int viewSize = -1;
for (int i = 0; i < comps.size(); i++)
{
}
String title = new String(this.getTitle());
- if (viewtitle!=null)
+ if (viewtitle != null)
+ {
+ title = viewtitle + " ( " + title + ")";
+ }
+ else
{
- title = viewtitle+" ( "+title+")";
- } else {
if (title.indexOf("(View") > -1)
{
title = title.substring(0, title.indexOf("(View"));
newaf.viewport.redoList = viewport.redoList;
return newaf;
}
+
/**
*
* @return list of feature groups on the view
public String[] getFeatureGroups()
{
FeatureRenderer fr = null;
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
return fr.getGroups();
}
return null;
}
+
/**
* get sequence feature groups that are hidden or shown
- * @param visible true is visible
+ *
+ * @param visible
+ * true is visible
* @return list
*/
public String[] getFeatureGroupsOfState(boolean visible)
{
FeatureRenderer fr = null;
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
return fr.getGroups(visible);
}
return null;
}
+
/**
* Change the display state for the given feature groups
- * @param groups list of group strings
- * @param state visible or invisible
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
*/
- public void setFeatureGroupState(String[] groups, boolean state) {
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
FeatureRenderer fr = null;
this.sequenceFeatures.setState(true);
viewport.showSequenceFeatures(true);
- if (alignPanel!=null && (fr=alignPanel.getFeatureRenderer())!=null)
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
{
fr.setGroupState(groups, state);
alignPanel.seqPanel.seqCanvas.repaint();
}
}
}
+
public void seqLimits_itemStateChanged()
{
viewport.setShowJVSuffix(seqLimits.getState());
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.getPreferredSize().width,
- overview.getPreferredSize().height + 50);
+ overview.getPreferredSize().width,
+ overview.getPreferredSize().height + 50);
frame.pack();
frame.addWindowListener(new WindowAdapter()
{
if (viewport.getAbovePIDThreshold())
{
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+ "Background");
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
Alignment al = (Alignment) viewport.alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3,
- al.getSequences(), 0,
- al.getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0, al
+ .getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
cs.setConservation(c);
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
- "Background"));
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
}
else
}
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.hiddenRepSequences),
- sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg
+ .getSequences(viewport.hiddenRepSequences), sg.getWidth());
}
else
{
try
{
sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
sg.cs = cs;
}
if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
+ || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg
+ .getSequences(viewport.hiddenRepSequences), 0, sg
+ .getWidth()));
}
else
{
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.
- hiddenRepSequences), 0,
- viewport.alignment.getWidth() - 1);
+ ResidueProperties.propHash, 3, sg
+ .getSequences(viewport.hiddenRepSequences), 0,
+ viewport.alignment.getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
alignPanel.getOverviewPanel().updateOverviewImage();
}
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .sequenceColoursChanged(alignPanel);
+ 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");
+ SliderPanel.setPIDSliderSource(alignPanel, viewport
+ .getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
protected void modifyConservation_actionPerformed()
{
- if (viewport.getConservationSelected() && viewport.globalColourScheme != null)
+ if (viewport.getConservationSelected()
+ && viewport.globalColourScheme != null)
{
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
- "Background");
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.globalColourScheme, "Background");
SliderPanel.showConservationSlider();
}
}
public void sortPairwiseMenuItem_actionPerformed()
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(),
- viewport.getAlignment().getSequenceAt(0), null);
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
+ 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.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.paintAlignment(true);
public void pairwiseAlignmentMenuItem_actionPerformed()
{
if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 1)
+ && viewport.getSelectionGroup().getSize() > 1)
{
Frame frame = new Frame();
frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
+ 500);
}
}
public void PCAMenuItem_actionPerformed()
{
- //are the sequences aligned?
+ // are the sequences aligned?
if (!viewport.alignment.isAligned())
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
alignPanel.paintAlignment(true);
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() < 4 &&
- viewport.getSelectionGroup().getSize() > 0)
- || viewport.getAlignment().getHeight() < 4)
+ if ((viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() < 4 && viewport
+ .getSelectionGroup().getSize() > 0)
+ || viewport.getAlignment().getHeight() < 4)
{
return;
}
try
{
new PCAPanel(viewport);
- }
- catch (java.lang.OutOfMemoryError ex)
+ } catch (java.lang.OutOfMemoryError ex)
{
}
void NewTreePanel(String type, String pwType, String title)
{
- //are the sequences aligned?
+ // are the sequences aligned?
if (!viewport.alignment.isAligned())
{
SequenceI current;
int Width = viewport.getAlignment().getWidth();
- for (int i = 0; i < viewport.getAlignment().getSequences().size();
- i++)
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
{
current = viewport.getAlignment().getSequenceAt(i);
}
- if ( (viewport.getSelectionGroup() != null &&
- viewport.getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null
- && viewport.alignment.getHeight() > 1))
+ if ((viewport.getSelectionGroup() != null && viewport
+ .getSelectionGroup().getSize() > 1)
+ || (viewport.getSelectionGroup() == null && viewport.alignment
+ .getHeight() > 1))
{
- final TreePanel tp = new TreePanel(viewport,
- type,
- pwType);
+ final TreePanel tp = new TreePanel(viewport, type, pwType);
addTreeMenuItem(tp, title);
public void loadTree(jalview.io.NewickFile tree, String treeFile)
{
- TreePanel tp = new TreePanel(viewport,
- treeFile,
- "From File - ",
- tree);
+ TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree);
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
addTreeMenuItem(tp, treeFile);
}
{
public void actionPerformed(ActionEvent evt)
{
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel
+ .getTree());
alignPanel.paintAlignment(true);
}
});
protected void about_actionPerformed()
{
- class AboutPanel
- extends Canvas
+ class AboutPanel extends Canvas
{
String version;
+
public AboutPanel(String version)
{
this.version = version;
int fh = fm.getHeight();
int y = 5, x = 7;
g.setColor(Color.black);
- // TODO: update this text for each release or centrally store it for lite and application
+ // TODO: update this text for each release or centrally store it for
+ // lite and application
g.setFont(new Font("Helvetica", Font.BOLD, 14));
g.drawString("JalviewLite - Release " + version, x, y += fh);
g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString("Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
- x, y += fh * 1.5);
- g.drawString("David Martin & Geoff Barton.",
- x+50, y += fh);
- g.drawString("Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", x,
- y += fh);
+ g
+ .drawString(
+ "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,",
+ x, y += fh * 1.5);
+ g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
+ g
+ .drawString(
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
+ x, y += fh);
+ g
+ .drawString(
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
+ x, y += fh);
g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
- x, y += fh);
- g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);
+ g.drawString(
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",x,y+=fh);
+ g.drawString("Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",x,y+=fh);
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",x,y+=fh);
}
}
try
{
BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ url.openStream()));
String line;
- while ( (line = reader.readLine()) != null)
+ while ((line = reader.readLine()) != null)
{
if (line.indexOf("VERSION") > -1)
{
version = line.substring(line.indexOf("=") + 1);
}
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
{
try
{
- System.out.println("Show url: " + url);
- viewport.applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
+ if (url.indexOf(":")==-1)
+ {
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL
+ if (url.indexOf("/")==0)
+ {
+ String codebase = viewport.applet.getCodeBase().toString();
+ url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url;
+ } else {
+ url = viewport.applet.getCodeBase()+url;
+ }
+ System.out.println("Show url (prepended codebase): " + url);
+ } else {
+ System.out.println("Show url: " + url);
+ }
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url), target);
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
}
- //////////////////////////////////////////////////////////////////////////////////
- //JBuilder Graphics here
-
- 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();
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ 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();
+
+ 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...");
+
+ 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 undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
MenuItem noColourmenuItem = new MenuItem();
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
MenuItem findMenuItem = new MenuItem();
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
- MenuItem nucleotideColour = 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();
+
+ 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();
+
+ 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();
- CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
- private void jbInit()
- throws Exception
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+ private void jbInit() throws Exception
{
setMenuBar(alignFrameMenuBar);
MenuItem item;
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
- i++)
+ 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()
{
pairwiseAlignmentMenuItem.addActionListener(this);
PCAMenuItem.setLabel("Principal Component Analysis");
PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem.setLabel(
- "Average Distance Using % Identity");
+ averageDistanceTreeMenuItem
+ .setLabel("Average Distance Using % Identity");
averageDistanceTreeMenuItem.addActionListener(this);
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
neighbourTreeMenuItem.addActionListener(this);
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62 Score");
BLOSUM62Colour.addActionListener(this);
- avDistanceTreeBlosumMenuItem.setLabel(
- "Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem
+ .setLabel("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem.addActionListener(this);
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
njTreeBlosumMenuItem.addActionListener(this);
inputText.addActionListener(this);
centreColumnLabelFlag.setLabel("Centre column labels");
centreColumnLabelFlag.addItemListener(this);
-
+
helpMenu.setLabel("Help");
documentation.setLabel("Documentation");
documentation.addActionListener(this);
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
}
+
MenuItem featureSettings = new MenuItem();
+
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+
MenuItem annotationColour = new MenuItem();
+
MenuItem invertColSel = new MenuItem();
+
Menu menu1 = new Menu();
+
MenuItem showColumns = new MenuItem();
+
MenuItem showSeqs = 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();
/**
- * Attach the alignFrame panels after embedding menus, if necessary.
- * This used to be called setEmbedded, but is now creates the
- * dropdown menus in a platform independent manner
- * to avoid OSX/Mac menu appendage daftness.
- *
- * @param reallyEmbedded true to attach the view to the applet area on the page rather than in a new window
+ * Attach the alignFrame panels after embedding menus, if necessary. This used
+ * to be called setEmbedded, but is now creates the dropdown menus in a
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.
+ *
+ * @param reallyEmbedded
+ * true to attach the view to the applet area on the page
+ * rather than in a new window
*/
public void createAlignFrameWindow(boolean reallyEmbedded, String title)
{
if (reallyEmbedded)
{
- //////
+ // ////
// Explicly build the embedded menu panel for the on-page applet
//
// view cannot be closed if its actually on the page
fileMenu.remove(closeMenuItem);
fileMenu.remove(3); // Remove Seperator
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", Font.PLAIN, 10, false); // use our own fonts.
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
+ Font.PLAIN, 10, false); // use our own fonts.
// and actually add the components to the applet area
viewport.applet.setLayout(new BorderLayout());
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
viewport.applet.add(statusBar, BorderLayout.SOUTH);
- alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height
+ alignPanel.setSize(viewport.applet.getSize().width, viewport.applet
+ .getSize().height
- embeddedMenu.HEIGHT - statusBar.HEIGHT);
viewport.applet.add(alignPanel, BorderLayout.CENTER);
viewport.applet.validate();
- } else {
- ////////
+ }
+ else
+ {
+ // //////
// test and embed menu bar if necessary.
//
- if (embedMenuIfNeeded(alignPanel)) {
+ if (embedMenuIfNeeded(alignPanel))
+ {
// adjust for status bar height too
- alignPanel.setSize(getSize().width,
- getSize().height
+ alignPanel.setSize(getSize().width, getSize().height
- statusBar.HEIGHT);
}
add(statusBar, BorderLayout.SOUTH);
add(alignPanel, BorderLayout.CENTER);
// and register with the applet so it can pass external API calls to us
jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
+ DEFAULT_HEIGHT);
}
}
}