/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
-
package jalview.appletgui;
import java.io.*;
import java.net.*;
import java.util.*;
+import java.applet.Applet;
import java.awt.*;
import java.awt.event.*;
+import org.jmol.api.JmolViewer;
+
import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
import jalview.commands.*;
import jalview.datamodel.*;
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();
}
viewport.updateConsensus(alignPanel);
annotationPanelMenuItem.setState(viewport.showAnnotation);
+ displayNonconservedMenuItem.setState(viewport.getShowunconserved());
seqLimits.setState(viewport.showJVSuffix);
{
sortPairwiseMenuItem_actionPerformed();
}
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
}
param = applet.getParameter("wrap");
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
-
try
{
param = applet.getParameter("windowWidth");
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);
+ if (viewport.featureSettings != null)
+ {
+ viewport.featureSettings.refreshTable();
+ }
alignPanel.paintAlignment(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_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_F:
+ if (evt.isControlDown())
+ {
+ findMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
- case KeyEvent.VK_H:
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.wrapAlignment)
{
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
- {
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- viewport.showAllHiddenSeqs();
- }
- }
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.wrapAlignment)
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
- }
- 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_PAGE_UP:
- if (viewport.wrapAlignment)
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
+
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
{
- alignPanel.scrollUp(true);
+ this.removeAllGapsMenuItem_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
+ removeGappedColumnMenuItem_actionPerformed();
}
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
{
- alignPanel.scrollUp(false);
+ invertColSel_actionPerformed();
}
else
{
- alignPanel.setScrollValues(viewport.startRes,
- viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
+ invertSequenceMenuItem_actionPerformed();
}
- break;
+ }
+ break;
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
- {
- undoMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_actionPerformed();
- }
- break;
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
+ }
+ alignPanel.paintAlignment(true);
+ }
- case KeyEvent.VK_R:
- if (evt.isControlDown())
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+ .getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
{
- trimAlignment(false);
- }
- break;
+ invertSequenceMenuItem_actionPerformed();
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
- 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;
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection and indicate it should be hidden.
+ invertColSel_actionPerformed();
+ toggleCols = true;
+ }
+ }
- case KeyEvent.VK_U:
- if (evt.isControlDown())
- {
- this.deleteGroups_actionPerformed();
- }
- break;
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hide = true;
+ viewport.hideAllSelectedSeqs();
+ }
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
+ viewport.showAllHiddenSeqs();
+ }
+ }
- case KeyEvent.VK_T:
- if (evt.isControlDown())
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ viewport.hideSelectedColumns();
+ if (!toggleSeqs)
{
- newView(null);
+ viewport.selectionGroup = sg;
}
- break;
-
+ }
+ else if (!hide)
+ {
+ viewport.showAllHiddenColumns();
+ }
}
- alignPanel.paintAlignment(true);
}
public void keyReleased(KeyEvent evt)
- {}
+ {
+ }
public void keyTyped(KeyEvent evt)
- {}
+ {
+ }
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == colourTextMenuItem)
+ if (evt.getSource() == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == colourTextMenuItem)
{
colourTextMenuItem_actionPerformed();
}
else if (evt.getSource() == autoCalculate)
{
viewport.autocalculateConsensus = autoCalculate.getState();
- } else if (evt.getSource() == this.centreColumnLabelFlag)
+ }
+ else if (evt.getSource() == this.centreColumnLabelFlag)
{
centreColumnLabelFlag_stateChanged();
}
-
+ else if (evt.getSource() == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+
alignPanel.paintAlignment(true);
}
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.followHighlight = followMouseOverFlag.getState();
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
+ }
+
private void centreColumnLabelFlag_stateChanged()
{
viewport.centreColumnLabels = centreColumnLabelFlag.getState();
{
delete_actionPerformed();
}
+ else if (source == grpsFromSelection)
+ {
+ makeGrpsFromSelection_actionPerformed();
+ }
else if (source == deleteGroups)
{
deleteGroups_actionPerformed();
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- else if (source == hideSequences && viewport.getSelectionGroup() != null)
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllSelection)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showAllHidden)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
}
else if (source == featureSettings)
{
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)
{
{
sortIDMenuItem_actionPerformed();
}
+ else if (source == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
else if (source == sortGroupMenuItem)
{
sortGroupMenuItem_actionPerformed();
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));
+ "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);
}
return annotation;
}
+ private Hashtable getDisplayedFeatureCols()
+ {
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ Hashtable fcols = new Hashtable();
+ Enumeration en = viewport.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ Object col = en.nextElement();
+ fcols.put(col, fr.featureColours.get(col));
+ }
+ return fcols;
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
if (format.equalsIgnoreCase("Jalview"))
{
features = new FeaturesFile().printJalviewFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
}
else
{
features = new FeaturesFile().printGFFFormat(
- viewport.alignment.getSequencesArray(),
- viewport.featuresDisplayed);
+ viewport.alignment.getSequencesArray(),
+ getDisplayedFeatureCols());
}
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("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");
try
{
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(); }
+ */
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.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)
{
}
}
+ protected void makeGrpsFromSelection_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ // alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
protected void deleteGroups_actionPerformed()
{
viewport.alignment.deleteAllGroups();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
+ public void invertColSel_actionPerformed()
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ }
+
void trimAlignment(boolean trimLeft)
{
ColumnSelection colSel = viewport.getColumnSelection();
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
{
}
}
- 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());
+ 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());
alignPanel.paintAlignment(true);
}
+ protected void displayNonconservedMenuItem_actionPerformed()
+ {
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
protected void wrapMenuItem_actionPerformed()
{
viewport.setWrapAlignment(wrapMenuItem.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.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.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));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.alignment));
alignPanel.paintAlignment(true);
}
public void sortGroupMenuItem_actionPerformed()
{
- // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
- // HistoryItem.SORT));
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.alignment));
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?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
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?
- if (!viewport.alignment.isAligned())
+ // are the sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
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);
}
- void addTreeMenuItem(final TreePanel treePanel, String title)
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
+ viewport.alignment));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
{
final MenuItem item = new MenuItem(title);
sortByTreeMenu.add(item);
{
public void actionPerformed(ActionEvent evt)
{
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
- alignPanel.paintAlignment(true);
+ sortByTree(treePanel, title); // treePanel.getTitle());
}
});
treePanel.addWindowListener(new WindowAdapter()
{
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
public void windowClosing(WindowEvent e)
{
sortByTreeMenu.remove(item);
protected void about_actionPerformed()
{
- class AboutPanel
- extends Canvas
+ class AboutPanel extends Canvas
{
String version;
- public AboutPanel(String version)
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
{
this.version = version;
+ this.builddate = builddate;
}
public void paint(Graphics g)
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
g.setFont(new Font("Helvetica", Font.BOLD, 14));
- g.drawString("Jalview - Release " + version, 200, y += fh);
+ g.drawString("JalviewLite - Release " + version, x, y += fh);
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));
+ g.drawString("Build date: " + builddate, x, 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);
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",
- x, y += fh);
g.drawString(
- "For any issues relating to Jalview, email help@jalview.org", 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);
- }
- }
-
- String version = "test";
- java.net.URL url = getClass().getResource("/.build_properties");
- if (url != null)
- {
- try
- {
- BufferedReader reader = new BufferedReader(new InputStreamReader(
- url.openStream()));
- String line;
- while ( (line = reader.readLine()) != null)
- {
- if (line.indexOf("VERSION") > -1)
- {
- version = line.substring(line.indexOf("=") + 1);
- }
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
+ "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(
+ "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);
}
}
Frame frame = new Frame();
- frame.add(new AboutPanel(version));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
}
{
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);
+ }
+ if (url.indexOf("javascript:") == 0)
+ {
+ // no target for the javascript context
+ viewport.applet.getAppletContext().showDocument(
+ new java.net.URL(url));
+ }
+ else
+ {
+ 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 sortLengthMenuItem = 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();
+
+ CheckboxMenuItem displayNonconservedMenuItem = 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 grpsFromSelection = 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();
+
+ CheckboxMenuItem followMouseOverFlag = 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()
{
sortPairwiseMenuItem.addActionListener(this);
sortIDMenuItem.setLabel("by ID");
sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel("by Length");
+ sortLengthMenuItem.addActionListener(this);
sortGroupMenuItem.setLabel("by Group");
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel("Remove Redundancy...");
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);
annotationPanelMenuItem.addItemListener(this);
colourTextMenuItem.setLabel("Colour Text");
colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel("Show nonconserved");
+ displayNonconservedMenuItem.addItemListener(this);
alProperties.addActionListener(this);
overviewMenuItem.setLabel("Overview Window");
overviewMenuItem.addActionListener(this);
nucleotideColour.addActionListener(this);
deleteGroups.setLabel("Undefine Groups");
deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel("Make Groups for selection");
+ grpsFromSelection.addActionListener(this);
copy.setLabel("Copy");
copy.addActionListener(this);
cut.setLabel("Cut");
inputText.addActionListener(this);
centreColumnLabelFlag.setLabel("Centre column labels");
centreColumnLabelFlag.addItemListener(this);
-
+ followMouseOverFlag.setLabel("Automatic Scrolling");
+ followMouseOverFlag.addItemListener(this);
helpMenu.setLabel("Help");
documentation.setLabel("Documentation");
documentation.addActionListener(this);
menu2.setLabel("Hide");
hideColumns.setLabel("Selected Columns");
hideSequences.setLabel("Selected Sequences");
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
+ hideAllSelection.setLabel("Selected Region");
+ showAllHidden.setLabel("All Sequences and Columns");
invertColSel.addActionListener(this);
showColumns.addActionListener(this);
showSeqs.addActionListener(this);
hideColumns.addActionListener(this);
hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
formatMenu.setLabel("Format");
selectMenu.setLabel("Select");
newView.setLabel("New View");
viewMenu.add(menu1);
viewMenu.add(menu2);
viewMenu.addSeparator();
+ viewMenu.add(followMouseOverFlag);
viewMenu.add(annotationPanelMenuItem);
viewMenu.addSeparator();
viewMenu.add(sequenceFeatures);
pasteMenu.add(pasteNew);
pasteMenu.add(pasteThis);
sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
sort.add(sortByTreeMenu);
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
helpMenu.add(about);
menu1.add(showColumns);
menu1.add(showSeqs);
+ menu1.add(showAllHidden);
menu2.add(hideColumns);
menu2.add(hideSequences);
+ menu2.add(hideAllSelection);
+ menu2.add(hideAllButSelection);
formatMenu.add(font);
formatMenu.add(seqLimits);
formatMenu.add(wrapMenuItem);
formatMenu.add(viewBoxesMenuItem);
formatMenu.add(viewTextMenuItem);
formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
formatMenu.add(renderGapsMenuItem);
formatMenu.add(centreColumnLabelFlag);
selectMenu.add(findMenuItem);
selectMenu.add(deselectAllSequenceMenuItem);
selectMenu.add(invertSequenceMenuItem);
selectMenu.add(invertColSel);
+ selectMenu.add(grpsFromSelection);
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();
+
+ MenuItem hideAllButSelection = new MenuItem();
+
+ MenuItem hideAllSelection = new MenuItem();
+
+ MenuItem showAllHidden = 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
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);
+ 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);
+ }
+ }
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+ *
+ public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
+ {
+ org.jmol.api.JmolViewer viewer=null;
+ try {
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ }
+ catch (ClassCastException ex) {
+ System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
+ }
+ if (viewer==null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs=null;
+ if (sequenceIds==null || sequenceIds.length==0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ } else {
+ Vector sqi=new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid=0;sid<sequenceIds.length;sid++) {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq!=null) {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size()>0) {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid=0,sSize=sqi.size();sid<sSize;sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ } else {
+ return null;
+ }
+ }
+ ExtJmol jmv=null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv==null){
+ // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, seqs);
+ }
+ return jmv;
+
+ }
+ **/
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getPDBId();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty()==null)
+ {pdbentry.setProperty(new Hashtable());}
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ }
+ }
+ return true;
+ }
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[] { seqs[i], (chains!=null) ? chains[i] : null});
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[] { seqs, chains};
+
+ }
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm!=null)
+ {
+ System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
+ }
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
}
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
}
}
git://source.jalview.org / jalview.git / blobdiff