-/*
- * 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.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.JalviewLite;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.structure.StructureSelectionManager;
-
-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)
- {
-
- if (applet != null)
- {
- jalviewServletURL = applet.getParameter("APPLICATION_URL");
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- viewport = new AlignViewport(al, applet);
- alignPanel = new AlignmentPanel(this, viewport);
-
- viewport.updateConservation(alignPanel);
- viewport.updateConsensus(alignPanel);
-
- annotationPanelMenuItem.setState(viewport.showAnnotation);
- displayNonconservedMenuItem.setState(viewport.getShowunconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
- showGroupConsensus.setState(viewport.showGroupConsensus);
- showGroupConservation.setState(viewport.showGroupConservation);
- showConsensusHistogram.setState(viewport.showConsensusHistogram);
- showSequenceLogo.setState(viewport.showSequenceLogo);
-
- seqLimits.setState(viewport.showJVSuffix);
-
- if (applet != null)
- {
- String param = applet.getParameter("sortBy");
- if (param != null)
- {
- if (param.equalsIgnoreCase("Id"))
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Pairwise Identity"))
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Length"))
- {
- sortLengthMenuItem_actionPerformed();
- }
- }
-
- param = applet.getParameter("wrap");
- if (param != null)
- {
- if (param.equalsIgnoreCase("true"))
- {
- wrapMenuItem.setState(true);
- wrapMenuItem_actionPerformed();
- }
- }
- param = applet.getParameter("centrecolumnlabels");
- if (param != null)
- {
- centreColumnLabelFlag.setState(true);
- centreColumnLabelFlag_stateChanged();
- }
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
-
- }
-
- // Some JVMS send keyevents to Top frame or lowest panel,
- // Havent worked out why yet. So add to both this frame and seqCanvas for
- // now
- this.addKeyListener(this);
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);
- alignPanel.idPanel.idCanvas.addKeyListener(this);
- alignPanel.scalePanel.addKeyListener(this);
- alignPanel.annotationPanel.addKeyListener(this);
- alignPanel.annotationPanelHolder.addKeyListener(this);
- alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
- alignPanel.alabels.addKeyListener(this);
- createAlignFrameWindow(embedded, title);
- alignPanel.validate();
- alignPanel.paintAlignment(true);
- }
-
- public AlignViewport getAlignViewport()
- {
- return viewport;
- }
-
- public SeqCanvas getSeqcanvas()
- {
- return alignPanel.seqPanel.seqCanvas;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param String
- * DOCUMENT ME!
- */
-
- public void parseFeaturesFile(String file, String type)
- {
- Hashtable featureLinks = new Hashtable();
- boolean featuresFile = false;
- try
- {
- featuresFile = new jalview.io.FeaturesFile(file, type)
- .parse(viewport.alignment,
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- if (featuresFile)
- {
- if (featureLinks.size() > 0)
- {
- 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());
-
- switch (evt.getKeyCode())
- {
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed();
-
- alignPanel.alabels.cancelDrag();
- 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_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_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_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_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_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- toggleHiddenRegions(toggleSeqs, toggleCols);
- break;
- }
-
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
- {
- undoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
-
- case KeyEvent.VK_R:
- if (evt.isControlDown())
- {
- trimAlignment(false);
- }
- break;
-
- case KeyEvent.VK_E:
- if (evt.isControlDown())
- {
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- }
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
- {
- if (evt.isAltDown())
- {
- invertColSel_actionPerformed();
- }
- else
- {
- invertSequenceMenuItem_actionPerformed();
- }
- }
- 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);
- }
-
- /**
- * 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)
- {
- invertSequenceMenuItem_actionPerformed();
- sg = viewport.getSelectionGroup();
- toggleSeqs = true;
-
- }
- 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;
- }
- }
-
- if (toggleSeqs)
- {
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())
- {
- hide = true;
- viewport.hideAllSelectedSeqs();
- }
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- viewport.showAllHiddenSeqs();
- }
- }
-
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- viewport.hideSelectedColumns();
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- viewport.showAllHiddenColumns();
- }
- }
- }
-
- public void keyReleased(KeyEvent evt)
- {
- }
-
- public void keyTyped(KeyEvent evt)
- {
- }
-
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt.getSource() == displayNonconservedMenuItem)
- {
- displayNonconservedMenuItem_actionPerformed();
- }
- else if (evt.getSource() == colourTextMenuItem)
- {
- colourTextMenuItem_actionPerformed();
- }
- else if (evt.getSource() == wrapMenuItem)
- {
- wrapMenuItem_actionPerformed();
- }
- else if (evt.getSource() == scaleAbove)
- {
- viewport.setScaleAboveWrapped(scaleAbove.getState());
- }
- else if (evt.getSource() == scaleLeft)
- {
- viewport.setScaleLeftWrapped(scaleLeft.getState());
- }
- else if (evt.getSource() == scaleRight)
- {
- viewport.setScaleRightWrapped(scaleRight.getState());
- }
- else if (evt.getSource() == seqLimits)
- {
- seqLimits_itemStateChanged();
- }
- else if (evt.getSource() == viewBoxesMenuItem)
- {
- viewport.setShowBoxes(viewBoxesMenuItem.getState());
- }
- else if (evt.getSource() == viewTextMenuItem)
- {
- viewport.setShowText(viewTextMenuItem.getState());
- }
- else if (evt.getSource() == renderGapsMenuItem)
- {
- viewport.setRenderGaps(renderGapsMenuItem.getState());
- }
- else if (evt.getSource() == annotationPanelMenuItem)
- {
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
- }
- else if (evt.getSource() == sequenceFeatures)
- {
- viewport.showSequenceFeatures(sequenceFeatures.getState());
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- else if (evt.getSource() == conservationMenuItem)
- {
- conservationMenuItem_actionPerformed();
- }
- else if (evt.getSource() == abovePIDThreshold)
- {
- abovePIDThreshold_actionPerformed();
- }
- else if (evt.getSource() == applyToAllGroups)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
- }
- else if (evt.getSource() == autoCalculate)
- {
- viewport.autocalculateConsensus = autoCalculate.getState();
- }
- else if (evt.getSource() == this.centreColumnLabelFlag)
- {
- centreColumnLabelFlag_stateChanged();
- }
- else if (evt.getSource() == this.followMouseOverFlag)
- {
- mouseOverFlag_stateChanged();
- }
- else if (evt.getSource() == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (evt.getSource() == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (evt.getSource() == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (evt.getSource() == showConsensusHistogram)
- {
- showConsensusHistogram_actionPerformed();
- }
- else if (evt.getSource() == applyAutoAnnotationSettings)
- {
- applyAutoAnnotationSettings_actionPerformed();
- }
- 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();
- this.alignPanel.annotationPanel.repaint();
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
-
- if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == loadTree)
- {
- loadTree_actionPerformed();
- }
- else if (source == loadApplication)
- {
- launchFullApplication();
- }
- else if (source == loadAnnotations)
- {
- loadAnnotations();
- }
- else if (source == outputAnnotations)
- {
- outputAnnotations(true);
- }
- else if (source == outputFeatures)
- {
- outputFeatures(true, "Jalview");
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == pasteNew)
- {
- pasteNew_actionPerformed();
- }
- else if (source == pasteThis)
- {
- pasteThis_actionPerformed();
- }
- else if (source == cut)
- {
- cut_actionPerformed();
- }
- else if (source == delete)
- {
- delete_actionPerformed();
- }
- else if (source == grpsFromSelection)
- {
- makeGrpsFromSelection_actionPerformed();
- }
- else if (source == deleteGroups)
- {
- deleteGroups_actionPerformed();
- }
- else if (source == selectAllSequenceMenuItem)
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == deselectAllSequenceMenuItem)
- {
- deselectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == invertSequenceMenuItem)
- {
- invertSequenceMenuItem_actionPerformed();
- }
- else if (source == invertColSel)
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- }
- else if (source == remove2LeftMenuItem)
- {
- trimAlignment(true);
- }
- else if (source == remove2RightMenuItem)
- {
- trimAlignment(false);
- }
- else if (source == removeGappedColumnMenuItem)
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- else if (source == removeAllGapsMenuItem)
- {
- removeAllGapsMenuItem_actionPerformed();
- }
- else if (source == findMenuItem)
- {
- findMenuItem_actionPerformed();
- }
- else if (source == font)
- {
- new FontChooser(alignPanel);
- }
- else if (source == newView)
- {
- newView(null);
- }
- else if (source == showColumns)
- {
- viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
- }
- 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)
- {
- 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 == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (source == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (source == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (source == showConsensusHistogram)
- {
- showConsensusHistogram_actionPerformed();
- }
- else if (source == applyAutoAnnotationSettings)
- {
- applyAutoAnnotationSettings_actionPerformed();
- }
- else if (source == featureSettings)
- {
- new FeatureSettings(alignPanel);
- }
- else if (source == alProperties)
- {
- StringBuffer contents = new jalview.io.AlignmentProperties(
- viewport.alignment).formatAsString();
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
- cap.setText(contents.toString());
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
- + getTitle(), 400, 250);
- }
- else if (source == overviewMenuItem)
- {
- overviewMenuItem_actionPerformed();
- }
- else if (source == noColourmenuItem)
- {
- changeColour(null);
- }
- else if (source == clustalColour)
- {
- abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(),
- viewport.alignment.getWidth()));
- }
- else if (source == zappoColour)
- {
- changeColour(new ZappoColourScheme());
- }
- else if (source == taylorColour)
- {
- changeColour(new TaylorColourScheme());
- }
- else if (source == hydrophobicityColour)
- {
- changeColour(new HydrophobicColourScheme());
- }
- else if (source == helixColour)
- {
- changeColour(new HelixColourScheme());
- }
- else if (source == strandColour)
- {
- changeColour(new StrandColourScheme());
- }
- else if (source == turnColour)
- {
- changeColour(new TurnColourScheme());
- }
- else if (source == buriedColour)
- {
- changeColour(new BuriedColourScheme());
- }
- else if (source == nucleotideColour)
- {
- changeColour(new NucleotideColourScheme());
- }
- else if (source == modifyPID)
- {
- modifyPID_actionPerformed();
- }
- else if (source == modifyConservation)
- {
- modifyConservation_actionPerformed();
- }
- else if (source == userDefinedColour)
- {
- new UserDefinedColours(alignPanel, null);
- }
- else if (source == PIDColour)
- {
- changeColour(new PIDColourScheme());
- }
- else if (source == BLOSUM62Colour)
- {
- changeColour(new Blosum62ColourScheme());
- }
- else if (source == annotationColour)
- {
- new AnnotationColourChooser(viewport, alignPanel);
- }
- else if (source == sortPairwiseMenuItem)
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (source == sortIDMenuItem)
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (source == sortLengthMenuItem)
- {
- sortLengthMenuItem_actionPerformed();
- }
- else if (source == sortGroupMenuItem)
- {
- sortGroupMenuItem_actionPerformed();
- }
- else if (source == removeRedundancyMenuItem)
- {
- removeRedundancyMenuItem_actionPerformed();
- }
- else if (source == pairwiseAlignmentMenuItem)
- {
- pairwiseAlignmentMenuItem_actionPerformed();
- }
- else if (source == PCAMenuItem)
- {
- PCAMenuItem_actionPerformed();
- }
- else if (source == averageDistanceTreeMenuItem)
- {
- averageDistanceTreeMenuItem_actionPerformed();
- }
- else if (source == neighbourTreeMenuItem)
- {
- neighbourTreeMenuItem_actionPerformed();
- }
- else if (source == njTreeBlosumMenuItem)
- {
- njTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == avDistanceTreeBlosumMenuItem)
- {
- avTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == documentation)
- {
- documentation_actionPerformed();
- }
- else if (source == about)
- {
- about_actionPerformed();
- }
-
- }
-
- public void inputText_actionPerformed()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
- }
-
- protected void outputText_actionPerformed(ActionEvent e)
- {
- 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));
- }
-
- public void loadAnnotations()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations file here.");
- cap.setAnnotationImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
-
- }
-
- public String outputAnnotations(boolean displayTextbox)
- {
- String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.alignment
- .getAlignmentAnnotation() : null, viewport.alignment
- .getGroups(),
- ((Alignment) viewport.alignment).alignmentProperties);
-
- if (displayTextbox)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
- cap.setText(annotation);
- }
-
- return annotation;
- }
-
- 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(),
- getDisplayedFeatureCols());
- }
- else
- {
- features = new FeaturesFile().printGFFFormat(
- 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);
-
- cap.setText(features);
- }
-
- return features;
- }
-
- void launchFullApplication()
- {
- StringBuffer url = new StringBuffer(jalviewServletURL);
-
- url.append("?open="
- + appendProtocol(viewport.applet.getParameter("file")));
-
- if (viewport.applet.getParameter("features") != null)
- {
- url.append("&features=");
- url.append(appendProtocol(viewport.applet.getParameter("features")));
- }
-
- if (viewport.applet.getParameter("annotations") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
- }
-
- if (viewport.applet.getParameter("jnetfile") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
- }
-
- if (viewport.applet.getParameter("defaultColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("defaultColour")));
- }
-
- if (viewport.applet.getParameter("userDefinedColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("userDefinedColour")));
- }
- if (viewport.applet.getParameter("tree") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("tree")));
- }
- if (viewport.applet.getParameter("treeFile") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("treeFile")));
- }
-
- showURL(url.toString(), "FULL_APP");
- }
-
- String removeWhiteSpace(String colour)
- {
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < colour.length(); i++)
- {
- if (Character.isWhitespace(colour.charAt(i)))
- {
- sb.append("%20");
- }
- else
- {
- sb.append(colour.charAt(i));
- }
- }
-
- return sb.toString();
- }
-
- String appendProtocol(String url)
- {
- try
- {
- new URL(url);
- 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;
- }
- return url;
- }
-
- public void closeMenuItem_actionPerformed()
- {
- PaintRefresher.RemoveComponent(alignPanel);
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
-
- if (PaintRefresher.components.size() == 0 && viewport.applet == null)
- {
- System.exit(0);
- }
-
- this.dispose();
- }
-
- /**
- * DOCUMENT ME!
- */
- void updateEditMenuBar()
- {
-
- if (viewport.historyList.size() > 0)
- {
- undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- }
-
- if (viewport.redoList.size() > 0)
- {
- redoMenuItem.setEnabled(true);
-
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- }
- }
-
- public void addHistoryItem(CommandI command)
- {
- if (command.getSize() > 0)
- {
- viewport.historyList.push(command);
- viewport.redoList.removeAllElements();
- updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void undoMenuItem_actionPerformed()
- {
- if (viewport.historyList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
- command.undoCommand(null);
-
- AlignViewport originalSource = getOriginatingSource(command);
-
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
- updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- originalSource.alignment.getSequences());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void redoMenuItem_actionPerformed()
- {
- if (viewport.redoList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
- command.doCommand(null);
-
- AlignViewport originalSource = getOriginatingSource(command);
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
-
- updateEditMenuBar();
- originalSource.firePropertyChange("alignment", null,
- 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
- AlignmentI al = null;
- if (command instanceof EditCommand)
- {
- EditCommand editCommand = (EditCommand) command;
- al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
- {
- originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
- break;
- }
- }
- }
- }
-
- if (originalSource == null)
- {
- // The original view is closed, we must validate
- // the current view against the closed view first
- if (al != null)
- {
- PaintRefresher.validateSequences(al, viewport.alignment);
- }
-
- originalSource = viewport;
- }
-
- return originalSource;
- }
-
- public void moveSelectedSequences(boolean up)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- if (up)
- {
- for (int i = 1; i < viewport.alignment.getHeight(); i++)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(null).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
- if (sg.getSequences(null).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i - 1);
- }
- }
- else
- {
- for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
- {
- SequenceI seq = viewport.alignment.getSequenceAt(i);
- if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
- {
- continue;
- }
-
- SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
- if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
- {
- continue;
- }
-
- viewport.alignment.getSequences().setElementAt(temp, i);
- viewport.alignment.getSequences().setElementAt(seq, i + 1);
- }
- }
-
- alignPanel.paintAlignment(true);
- }
-
- synchronized void slideSequences(boolean right, int size)
- {
- Vector sg = new Vector();
- if (viewport.cursorMode)
- {
- sg.addElement(viewport.alignment
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
- }
- else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport.alignment
- .getHeight())
- {
- sg = viewport.getSelectionGroup().getSequences(
- viewport.hiddenRepSequences);
- }
-
- if (sg.size() < 1)
- {
- return;
- }
-
- Vector invertGroup = new Vector();
-
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
- {
- if (!sg.contains(viewport.alignment.getSequenceAt(i)))
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));
- }
-
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
-
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
- for (int i = 0; i < invertGroup.size(); i++)
- seqs2[i] = (SequenceI) invertGroup.elementAt(i);
-
- SlideSequencesCommand ssc;
- if (right)
- ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
- size, viewport.getGapCharacter());
- else
- ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
- size, viewport.getGapCharacter());
-
- int groupAdjustment = 0;
- if (ssc.getGapsInsertedBegin() && right)
- {
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(size, 0);
- else
- groupAdjustment = size;
- }
- else if (!ssc.getGapsInsertedBegin() && !right)
- {
- if (viewport.cursorMode)
- alignPanel.seqPanel.moveCursor(-size, 0);
- else
- groupAdjustment = -size;
- }
-
- if (groupAdjustment != 0)
- {
- viewport.getSelectionGroup().setStartRes(
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);
- viewport.getSelectionGroup().setEndRes(
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);
- }
-
- boolean appendHistoryItem = false;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
- {
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
- .peek());
- }
-
- if (!appendHistoryItem)
- addHistoryItem(ssc);
-
- repaint();
- }
-
- static StringBuffer copiedSequences;
-
- static Vector copiedHiddenColumns;
-
- protected void copy_actionPerformed()
- {
- if (viewport.getSelectionGroup() == null)
- {
- return;
- }
-
- SequenceGroup sg = viewport.getSelectionGroup();
- copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.alignment.findIndex(seq);
- orderedSeqs.put(index + "", seq);
- }
-
- int index = 0, startRes, endRes;
- char ch;
-
- if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
- {
- copiedHiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
- else
- {
- copiedHiddenColumns = null;
- }
-
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = null;
-
- while (seq == null)
- {
- if (orderedSeqs.containsKey(index + ""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
-
- break;
- }
- else
- {
- index++;
- }
- }
-
- // FIND START RES
- // Returns residue following index if gap
- startRes = seq.findPosition(sg.getStartRes());
-
- // FIND END RES
- // Need to find the residue preceeding index if gap
- endRes = 0;
-
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap((ch)))
- {
- endRes++;
- }
- }
-
- if (endRes > 0)
- {
- endRes += seq.getStart() - 1;
- }
-
- copiedSequences.append(seq.getName()
- + "\t"
- + startRes
- + "\t"
- + endRes
- + "\t"
- + seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
- }
-
- }
-
- protected void pasteNew_actionPerformed()
- {
- paste(true);
- }
-
- protected void pasteThis_actionPerformed()
- {
- paste(false);
- }
-
- void paste(boolean newAlignment)
- {
- try
- {
-
- if (copiedSequences == null)
- {
- return;
- }
-
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
- Vector seqs = new Vector();
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- int start = Integer.parseInt(st.nextToken());
- int end = Integer.parseInt(st.nextToken());
- seqs.addElement(new Sequence(name, st.nextToken(), start, end));
- }
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- newSeqs[i] = (SequenceI) seqs.elementAt(i);
- }
-
- if (newAlignment)
- {
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
- {
- newtitle = getTitle();
- }
- else
- {
- newtitle = newtitle.concat("- from " + getTitle());
- }
- AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
-
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- else
- {
- addSequences(newSeqs);
- }
-
- } catch (Exception ex)
- {
- } // could be anything being pasted in here
-
- }
-
- void addSequences(SequenceI[] seqs)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- viewport.alignment.addSequence(seqs[i]);
- }
-
- // !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
- seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
-
- viewport.setEndSeq(viewport.alignment.getHeight());
- viewport.alignment.getWidth();
- viewport.firePropertyChange("alignment", null,
- viewport.alignment.getSequences());
-
- }
-
- protected void cut_actionPerformed()
- {
- copy_actionPerformed();
- delete_actionPerformed();
- }
-
- protected void delete_actionPerformed()
- {
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- Vector seqs = new Vector();
- SequenceI seq;
- for (int i = 0; i < sg.getSize(); i++)
- {
- seq = sg.getSequenceAt(i);
- seqs.addElement(seq);
- }
-
- // If the cut affects all sequences, remove highlighted columns
- if (sg.getSize() == viewport.alignment.getHeight())
- {
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
-
- SequenceI[] cut = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- cut[i] = (SequenceI) seqs.elementAt(i);
- }
-
- /*
- * //ADD HISTORY ITEM
- */
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.alignment));
-
- viewport.setSelectionGroup(null);
- viewport.alignment.deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- if (viewport.getAlignment().getHeight() < 1)
- {
- this.setVisible(false);
- }
- viewport.sendSelection();
- }
-
- /**
- * group consensus toggled
- *
- */
- protected void showGroupConsensus_actionPerformed()
- {
- viewport.setShowGroupConsensus(showGroupConsensus.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-
- }
-
- /**
- * group conservation toggled.
- */
- protected void showGroupConservation_actionPerformed()
- {
- viewport.setShowGroupConservation(showGroupConservation.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- protected void showConsensusHistogram_actionPerformed()
- {
- viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
- * .event.ActionEvent)
- */
- protected void showSequenceLogo_actionPerformed()
- {
- viewport.setShowSequenceLogo(showSequenceLogo.getState());
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- protected void applyAutoAnnotationSettings_actionPerformed()
- {
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
- }
-
- 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();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
-
- alignPanel.paintAlignment(true);
- }
-
- public void selectAllSequenceMenuItem_actionPerformed()
- {
- SequenceGroup sg = new SequenceGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
- sg.setEndRes(viewport.alignment.getWidth() - 1);
- viewport.setSelectionGroup(sg);
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void deselectAllSequenceMenuItem_actionPerformed()
- {
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.keyboardNo1 = null;
- alignPanel.seqPanel.keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.idPanel.idCanvas.searchResults = null;
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void invertSequenceMenuItem_actionPerformed()
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
- }
-
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- public void invertColSel_actionPerformed()
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
- }
-
- void trimAlignment(boolean trimLeft)
- {
- ColumnSelection colSel = viewport.getColumnSelection();
- int column;
-
- if (colSel.size() > 0)
- {
- if (trimLeft)
- {
- column = colSel.getMin();
- }
- else
- {
- column = colSel.getMax();
- }
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
- }
- else
- {
- seqs = viewport.alignment.getSequencesArray();
- }
-
- TrimRegionCommand trimRegion;
- if (trimLeft)
- {
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
- viewport.setStartRes(0);
- }
- else
- {
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.alignment, viewport.colSel,
- viewport.selectionGroup);
- }
-
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
-
- addHistoryItem(trimRegion);
-
- Vector groups = viewport.alignment.getGroups();
-
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if ((trimLeft && !sg.adjustForRemoveLeft(column))
- || (!trimLeft && !sg.adjustForRemoveRight(column)))
- {
- viewport.alignment.deleteGroup(sg);
- }
- }
-
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- }
-
- public void removeGappedColumnMenuItem_actionPerformed()
- {
- int start = 0, end = viewport.alignment.getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.alignment.getSequencesArray();
- }
-
- RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
- "Remove Gapped Columns", seqs, start, end, viewport.alignment);
-
- addHistoryItem(removeGapCols);
-
- statusBar.setText("Removed " + removeGapCols.getSize()
- + " empty columns.");
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
- // ShiftList shifts;
- // viewport.getAlignment().removeGaps(shifts=new ShiftList());
- // edit.alColumnChanges=shifts.getInverse();
- // if (viewport.hasHiddenColumns)
- // viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- public void removeAllGapsMenuItem_actionPerformed()
- {
- int start = 0, end = viewport.alignment.getWidth() - 1;
-
- SequenceI[] seqs;
- if (viewport.getSelectionGroup() != null)
- {
- seqs = viewport.getSelectionGroup().getSequencesAsArray(
- viewport.hiddenRepSequences);
- start = viewport.getSelectionGroup().getStartRes();
- end = viewport.getSelectionGroup().getEndRes();
- }
- else
- {
- seqs = viewport.alignment.getSequencesArray();
- }
-
- // This is to maintain viewport position on first residue
- // of first sequence
- SequenceI seq = viewport.alignment.getSequenceAt(0);
- int startRes = seq.findPosition(viewport.startRes);
-
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
- viewport.alignment));
-
- viewport.setStartRes(seq.findIndex(startRes) - 1);
-
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
-
- }
-
- public void findMenuItem_actionPerformed()
- {
- new Finder(alignPanel);
- }
-
- /**
- * create a new view derived from the current view
- *
- * @param viewtitle
- * @return frame for the new view
- */
- public AlignFrame newView(String viewtitle)
- {
- AlignmentI newal;
- if (viewport.hasHiddenRows)
- {
- newal = new Alignment(viewport.getAlignment().getHiddenSequences()
- .getFullAlignment().getSequencesArray());
- }
- else
- {
- newal = new Alignment(viewport.alignment.getSequencesArray());
- }
-
- if (viewport.alignment.getAlignmentAnnotation() != null)
- {
- for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
- {
- if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
- {
- newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
- }
- }
- }
-
- AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
-
- newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
- PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel,
- newaf.alignPanel.av.getSequenceSetId());
-
- PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
- newaf.alignPanel.av.getSequenceSetId());
- PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
- newaf.alignPanel.av.getSequenceSetId());
-
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- int viewSize = -1;
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- viewSize++;
- }
- }
-
- String title = new String(this.getTitle());
- if (viewtitle != null)
- {
- title = viewtitle + " ( " + title + ")";
- }
- else
- {
- if (title.indexOf("(View") > -1)
- {
- title = title.substring(0, title.indexOf("(View"));
- }
- title += "(View " + viewSize + ")";
- }
-
- newaf.setTitle(title.toString());
-
- newaf.viewport.historyList = viewport.historyList;
- 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)
- {
- return fr.getGroups();
- }
- return null;
- }
-
- /**
- * get sequence feature groups that are hidden or shown
- *
- * @param visible
- * true is visible
- * @return list
- */
- public String[] getFeatureGroupsOfState(boolean visible)
- {
- FeatureRenderer fr = 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
- */
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- FeatureRenderer fr = null;
- this.sequenceFeatures.setState(true);
- viewport.showSequenceFeatures(true);
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- fr.setGroupState(groups, state);
- alignPanel.seqPanel.seqCanvas.repaint();
- if (alignPanel.overviewPanel != null)
- {
- alignPanel.overviewPanel.updateOverviewImage();
- }
- }
- }
-
- public void seqLimits_itemStateChanged()
- {
- viewport.setShowJVSuffix(seqLimits.getState());
- alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
- }
-
- protected void colourTextMenuItem_actionPerformed()
- {
- viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void displayNonconservedMenuItem_actionPerformed()
- {
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void wrapMenuItem_actionPerformed()
- {
- viewport.setWrapAlignment(wrapMenuItem.getState());
- alignPanel.setWrapAlignment(wrapMenuItem.getState());
- scaleAbove.setEnabled(wrapMenuItem.getState());
- scaleLeft.setEnabled(wrapMenuItem.getState());
- scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- public void overviewMenuItem_actionPerformed()
- {
- if (alignPanel.overviewPanel != null)
- {
- return;
- }
-
- Frame frame = new Frame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- 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);
-
- frame.pack();
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
-
- alignPanel.setOverviewPanel(overview);
-
- }
-
- void changeColour(ColourSchemeI cs)
- {
- int threshold = 0;
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
-
- Alignment al = (Alignment) viewport.alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
-
- }
- else
- {
- cs.setConservation(null);
- }
-
- cs.setConsensus(viewport.hconsensus);
-
- }
- viewport.setGlobalColourScheme(cs);
-
- if (viewport.getColourAppliesToAllGroups())
- {
- Vector groups = viewport.alignment.getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (cs == null)
- {
- sg.cs = null;
- continue;
- }
- if (cs instanceof ClustalxColourScheme)
- {
- sg.cs = new ClustalxColourScheme(
- sg.getSequences(viewport.hiddenRepSequences),
- sg.getWidth());
- }
- else
- {
- try
- {
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- sg.cs = cs;
- }
- }
-
- if (viewport.getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(viewport.hiddenRepSequences), 0,
- sg.getWidth()));
- }
- else
- {
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(viewport.hiddenRepSequences), 0,
- viewport.alignment.getWidth() - 1);
- c.calculate();
- c.verdict(false, viewport.ConsPercGaps);
- sg.cs.setConservation(c);
- }
- else
- {
- sg.cs.setConservation(null);
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- }
- }
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(
- alignPanel);
-
- alignPanel.paintAlignment(true);
- }
-
- protected void modifyPID_actionPerformed()
- {
- if (viewport.getAbovePIDThreshold()
- && viewport.globalColourScheme != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- protected void modifyConservation_actionPerformed()
- {
- if (viewport.getConservationSelected()
- && viewport.globalColourScheme != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.globalColourScheme, "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
- protected void conservationMenuItem_actionPerformed()
- {
- viewport.setConservationSelected(conservationMenuItem.getState());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setState(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed();
- }
-
- public void abovePIDThreshold_actionPerformed()
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
- conservationMenuItem.setState(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed();
- }
-
- public void sortPairwiseMenuItem_actionPerformed()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
-
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
- }
-
- public void sortIDMenuItem_actionPerformed()
- {
- 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()
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.alignment));
- alignPanel.paintAlignment(true);
-
- }
-
- public void removeRedundancyMenuItem_actionPerformed()
- {
- new RedundancyPanel(alignPanel);
- }
-
- public void pairwiseAlignmentMenuItem_actionPerformed()
- {
- if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() > 1)
- {
- Frame frame = new Frame();
- frame.add(new PairwiseAlignPanel(alignPanel));
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
- 500);
- }
- }
-
- public void PCAMenuItem_actionPerformed()
- {
- // 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++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength() < Width)
- {
- current.insertCharAt(Width - 1, viewport.getGapCharacter());
- }
- }
- alignPanel.paintAlignment(true);
- }
-
- 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)
- {
- }
-
- }
-
- public void averageDistanceTreeMenuItem_actionPerformed()
- {
- NewTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- public void neighbourTreeMenuItem_actionPerformed()
- {
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- protected void njTreeBlosumMenuItem_actionPerformed()
- {
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed()
- {
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- void NewTreePanel(String type, String pwType, String title)
- {
- // 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++)
- {
- current = viewport.getAlignment().getSequenceAt(i);
-
- if (current.getLength() < Width)
- {
- current.insertCharAt(Width - 1, viewport.getGapCharacter());
- }
- }
- alignPanel.paintAlignment(true);
-
- }
-
- if ((viewport.getSelectionGroup() != null && viewport
- .getSelectionGroup().getSize() > 1)
- || (viewport.getSelectionGroup() == null && viewport.alignment
- .getHeight() > 1))
- {
- final TreePanel tp = new TreePanel(alignPanel, type, pwType);
-
- addTreeMenuItem(tp, title);
-
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
- }
- }
-
- void loadTree_actionPerformed()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your Newick tree file here.");
- cap.setTreeImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
- }
-
- public void loadTree(jalview.io.NewickFile tree, String treeFile)
- {
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
- addTreeMenuItem(tp, treeFile);
- }
-
- /**
- * 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);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- 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);
- };
- });
- }
- public boolean sortBy(AlignmentOrder alorder, String undoname)
- {
- SequenceI[] oldOrder = viewport.getAlignment()
- .getSequencesArray();
- if (viewport.applet.debug)
- {
- System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");
- }
- AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
- if (undoname!=null)
- {
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
- }
- alignPanel.paintAlignment(true);
- return true;
- }
- protected void documentation_actionPerformed()
- {
- showURL("http://www.jalview.org/help.html", "HELP");
- }
-
- protected void about_actionPerformed()
- {
-
- class AboutPanel extends Canvas
- {
- String version;
-
- String builddate;
-
- public AboutPanel(String version, String builddate)
- {
- this.version = version;
- this.builddate = builddate;
- }
-
- public void paint(Graphics g)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- FontMetrics fm = g.getFontMetrics();
- 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("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: Jim Procter, Andrew Waterhouse, 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(JalviewLite.getVersion(), JalviewLite
- .getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
-
- }
-
- public void showURL(String url, String target)
- {
- if (viewport.applet == null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- try
- {
- 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 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();
-
- MenuItem njTreeBlosumMenuItem = new MenuItem();
-
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
-
- 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 noColourmenuItem = new MenuItem();
-
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-
- MenuItem findMenuItem = new MenuItem();
-
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-
- MenuItem nucleotideColour = new MenuItem();
-
- MenuItem deleteGroups = new MenuItem();
-
- MenuItem 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();
-
- MenuItem modifyPID = new MenuItem();
-
- MenuItem modifyConservation = new MenuItem();
-
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
-
- Menu sortByTreeMenu = new Menu();
-
- Menu sort = new Menu();
-
- Menu calculate = new Menu();
-
- MenuItem inputText = new MenuItem();
-
- Menu helpMenu = new Menu();
-
- MenuItem documentation = new MenuItem();
-
- MenuItem about = new MenuItem();
-
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();
-
- CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
- CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
- Menu autoAnnMenu=new Menu();
- CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();
- CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
- CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
- CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
- CheckboxMenuItem showGroupConservation = 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++)
- {
-
- item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- outputText_actionPerformed(e);
- }
- });
-
- outputTextboxMenu.add(item);
- }
- closeMenuItem.addActionListener(this);
- loadApplication.addActionListener(this);
-
- loadTree.addActionListener(this);
- loadAnnotations.addActionListener(this);
- outputFeatures.addActionListener(this);
- outputAnnotations.addActionListener(this);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
- sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel("Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(this);
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
-
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
- grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
- modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
- autoCalculate.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel("Centre column labels");
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
-
- about.setLabel("About...");
- about.addActionListener(this);
- seqLimits.setState(true);
- seqLimits.setLabel("Show Sequence Limits");
- seqLimits.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- annotationColour.setLabel("by Annotation...");
- annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");
- invertColSel.setLabel("Invert Column Selection");
- menu1.setLabel("Show");
- showColumns.setLabel("All Columns ");
- showSeqs.setLabel("All Sequences");
- 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");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
- applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("Autocalculated Annotation");
-
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- hideAllButSelection.addActionListener(this);
- hideAllSelection.addActionListener(this);
- showAllHidden.addActionListener(this);
- showGroupConsensus.addItemListener(this);
- showGroupConservation.addItemListener(this);
- showConsensusHistogram.addItemListener(this);
- showSequenceLogo.addItemListener(this);
- applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
- newView.addActionListener(this);
- alignFrameMenuBar.add(fileMenu);
- alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(selectMenu);
- alignFrameMenuBar.add(viewMenu);
- alignFrameMenuBar.add(formatMenu);
- alignFrameMenuBar.add(colourMenu);
- alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(helpMenu);
-
- fileMenu.add(inputText);
- fileMenu.add(loadTree);
- fileMenu.add(loadAnnotations);
-
- fileMenu.addSeparator();
- fileMenu.add(outputTextboxMenu);
- fileMenu.add(outputFeatures);
- fileMenu.add(outputAnnotations);
-
- if (jalviewServletURL != null)
- {
- fileMenu.add(loadApplication);
- }
-
- fileMenu.addSeparator();
- fileMenu.add(closeMenuItem);
-
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.add(cut);
- editMenu.add(copy);
- editMenu.add(pasteMenu);
- editMenu.add(delete);
- editMenu.addSeparator();
- editMenu.add(remove2LeftMenuItem);
- editMenu.add(remove2RightMenuItem);
- editMenu.add(removeGappedColumnMenuItem);
- editMenu.add(removeAllGapsMenuItem);
- editMenu.add(removeRedundancyMenuItem);
- viewMenu.add(newView);
- viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
- viewMenu.addSeparator();
- viewMenu.add(followMouseOverFlag);
- viewMenu.add(annotationPanelMenuItem);
- autoAnnMenu.add(applyAutoAnnotationSettings);
- autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showSequenceLogo);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
- viewMenu.addSeparator();
- viewMenu.add(sequenceFeatures);
- viewMenu.add(featureSettings);
- viewMenu.addSeparator();
- viewMenu.add(alProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
- calculateMenu.addSeparator();
- calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
- calculateMenu.add(autoCalculate);
- this.add(statusBar, BorderLayout.SOUTH);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- helpMenu.add(documentation);
- helpMenu.add(about);
- menu1.add(showColumns);
- menu1.add(showSeqs);
- 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(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(viewBoxesMenuItem);
- formatMenu.add(viewTextMenuItem);
- formatMenu.add(colourTextMenuItem);
- formatMenu.add(displayNonconservedMenuItem);
- formatMenu.add(renderGapsMenuItem);
- formatMenu.add(centreColumnLabelFlag);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- 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
- */
- 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.
- // 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.add(alignPanel, BorderLayout.CENTER);
- final AlignFrame me = this;
- viewport.applet.addFocusListener(new FocusListener()
- {
-
- @Override
- public void focusLost(FocusEvent e)
- {
- if (me.viewport.applet.currentAlignFrame==me) {
- me.viewport.applet.currentAlignFrame = null;
- }}
-
- @Override
- public void focusGained(FocusEvent e)
- {
- me.viewport.applet.currentAlignFrame = me;
- }
- });
- viewport.applet.validate();
- }
- else
- {
- // //////
- // test and embed menu bar if necessary.
- //
- if (embedMenuIfNeeded(alignPanel))
- {
- // adjust for status bar height too
- 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);
- }
- }
-
- /**
- * 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 This method doesn't work
- * without an additional javascript library to exchange messages between the
- * distinct applets. See http://issues.jalview.org/browse/JAL-621
- *
- * @param viewer
- * JmolViewer instance
- * @param sequenceIds
- * - sequence Ids to search for associations
- */
- 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, new SequenceI[][] {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.useXtrnalSviewer)
- {
- // register the association(s) and quit, don't create any windows.
- StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
- 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.");
- }
-
- /**
- * modify the current selection, providing the user has not made a selection already.
- * @param sel - sequences from this alignment
- * @param csel - columns to be selected on the alignment
- */
- public void select(SequenceGroup sel, ColumnSelection csel)
- {
- alignPanel.seqPanel.selection(sel, csel, null);
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import java.net.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
+ ItemListener, KeyListener\r
+{\r
+ public AlignmentPanel alignPanel;\r
+\r
+ public AlignViewport viewport;\r
+\r
+ int DEFAULT_WIDTH = 700;\r
+\r
+ int DEFAULT_HEIGHT = 500;\r
+\r
+ String jalviewServletURL;\r
+\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
+ String title, boolean embedded)\r
+ {\r
+\r
+ if (applet != null)\r
+ {\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ viewport = new AlignViewport(al, applet);\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+ viewport.updateConservation(alignPanel);\r
+ viewport.updateConsensus(alignPanel);\r
+\r
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+ displayNonconservedMenuItem.setState(viewport.getShowunconserved());\r
+ followMouseOverFlag.setState(viewport.getFollowHighlight());\r
+ showGroupConsensus.setState(viewport.showGroupConsensus);\r
+ showGroupConservation.setState(viewport.showGroupConservation);\r
+ showConsensusHistogram.setState(viewport.showConsensusHistogram);\r
+ showSequenceLogo.setState(viewport.showSequenceLogo);\r
+\r
+ seqLimits.setState(viewport.showJVSuffix);\r
+\r
+ if (applet != null)\r
+ {\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (param.equalsIgnoreCase("Length"))\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
+ }\r
+\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ param = applet.getParameter("centrecolumnlabels");\r
+ if (param != null)\r
+ {\r
+ centreColumnLabelFlag.setState(true);\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
+ try\r
+ {\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ DEFAULT_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
+ {\r
+ int height = Integer.parseInt(param);\r
+ DEFAULT_HEIGHT = height;\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ }\r
+\r
+ // Some JVMS send keyevents to Top frame or lowest panel,\r
+ // Havent worked out why yet. So add to both this frame and seqCanvas for\r
+ // now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+ alignPanel.scalePanel.addKeyListener(this);\r
+ alignPanel.annotationPanel.addKeyListener(this);\r
+ alignPanel.annotationPanelHolder.addKeyListener(this);\r
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);\r
+ alignPanel.alabels.addKeyListener(this);\r
+ createAlignFrameWindow(embedded, title);\r
+ alignPanel.validate();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param String\r
+ * DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file, String type)\r
+ {\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try\r
+ {\r
+ featuresFile = new jalview.io.FeaturesFile(file, type)\r
+ .parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
+ featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (featuresFile)\r
+ {\r
+ if (featureLinks.size() > 0)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
+ }\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ if (viewport.featureSettings != null)\r
+ {\r
+ viewport.featureSettings.refreshTable();\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ }\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode\r
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
+ && Character.isDigit(evt.getKeyChar()))\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ \r
+ alignPanel.alabels.cancelDrag(); \r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ paste(evt.isShiftDown());\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(-1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = !viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "\r
+ + (viewport.cursorMode ? "on" : "off"));\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ toggleHiddenRegions(toggleSeqs, toggleCols);\r
+ break;\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(true);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(false);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ {\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ {\r
+ invertColSel_actionPerformed();\r
+ }\r
+ else\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView(null);\r
+ }\r
+ break;\r
+\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * called by key handler and the hide all/show all menu items\r
+ * \r
+ * @param toggleSeqs\r
+ * @param toggleCols\r
+ */\r
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
+ {\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (!toggleSeqs && !toggleCols)\r
+ {\r
+ // Hide everything by the current selection - this is a hack - we do the\r
+ // invert and then hide\r
+ // first check that there will be visible columns after the invert.\r
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel\r
+ .getSelected().size() > 0)\r
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
+ .getEndRes()))\r
+ {\r
+ // now invert the sequence set, if required - empty selection implies\r
+ // that no hiding is required.\r
+ if (sg != null)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ sg = viewport.getSelectionGroup();\r
+ toggleSeqs = true;\r
+\r
+ }\r
+ viewport.expandColSelection(sg, true);\r
+ // finally invert the column selection and get the new sequence\r
+ // selection and indicate it should be hidden.\r
+ invertColSel_actionPerformed();\r
+ toggleCols = true;\r
+ }\r
+ }\r
+\r
+ if (toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ }\r
+\r
+ if (toggleCols)\r
+ {\r
+ if (viewport.colSel.getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if (!toggleSeqs)\r
+ {\r
+ viewport.selectionGroup = sg;\r
+ }\r
+ }\r
+ else if (!hide)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void keyReleased(KeyEvent evt)\r
+ {\r
+ }\r
+\r
+ public void keyTyped(KeyEvent evt)\r
+ {\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt.getSource() == displayNonconservedMenuItem)\r
+ {\r
+ displayNonconservedMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == colourTextMenuItem)\r
+ {\r
+ colourTextMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == wrapMenuItem)\r
+ {\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == scaleAbove)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+ }\r
+ else if (evt.getSource() == scaleLeft)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+ }\r
+ else if (evt.getSource() == scaleRight)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
+ }\r
+ else if (evt.getSource() == seqLimits)\r
+ {\r
+ seqLimits_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == viewBoxesMenuItem)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == viewTextMenuItem)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == renderGapsMenuItem)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == annotationPanelMenuItem)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if (evt.getSource() == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == abovePIDThreshold)\r
+ {\r
+ abovePIDThreshold_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyToAllGroups)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ }\r
+ else if (evt.getSource() == autoCalculate)\r
+ {\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+ }\r
+ else if (evt.getSource() == this.centreColumnLabelFlag)\r
+ {\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == this.followMouseOverFlag)\r
+ {\r
+ mouseOverFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ private void mouseOverFlag_stateChanged()\r
+ {\r
+ viewport.followHighlight = followMouseOverFlag.getState();\r
+ // TODO: could kick the scrollTo mechanism to reset view for current\r
+ // searchresults.\r
+ }\r
+\r
+ private void centreColumnLabelFlag_stateChanged()\r
+ {\r
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();\r
+ this.alignPanel.annotationPanel.repaint();\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+\r
+ if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == loadTree)\r
+ {\r
+ loadTree_actionPerformed();\r
+ }\r
+ else if (source == loadApplication)\r
+ {\r
+ launchFullApplication();\r
+ }\r
+ else if (source == loadAnnotations)\r
+ {\r
+ loadAnnotations();\r
+ }\r
+ else if (source == outputAnnotations)\r
+ {\r
+ outputAnnotations(true);\r
+ }\r
+ else if (source == outputFeatures)\r
+ {\r
+ outputFeatures(true, "Jalview");\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == pasteNew)\r
+ {\r
+ pasteNew_actionPerformed();\r
+ }\r
+ else if (source == pasteThis)\r
+ {\r
+ pasteThis_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ else if (source == delete)\r
+ {\r
+ delete_actionPerformed();\r
+ }\r
+ else if (source == grpsFromSelection)\r
+ {\r
+ makeGrpsFromSelection_actionPerformed();\r
+ }\r
+ else if (source == deleteGroups)\r
+ {\r
+ deleteGroups_actionPerformed();\r
+ }\r
+ else if (source == selectAllSequenceMenuItem)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == deselectAllSequenceMenuItem)\r
+ {\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertSequenceMenuItem)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertColSel)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == remove2LeftMenuItem)\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ else if (source == remove2RightMenuItem)\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ else if (source == removeGappedColumnMenuItem)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeAllGapsMenuItem)\r
+ {\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else if (source == findMenuItem)\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ else if (source == font)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
+ else if (source == newView)\r
+ {\r
+ newView(null);\r
+ }\r
+ else if (source == showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideSequences\r
+ && viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllButSelection)\r
+ {\r
+ toggleHiddenRegions(false, false);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllSelection)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ viewport.expandColSelection(sg, false);\r
+ viewport.hideAllSelectedSeqs();\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showAllHidden)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (source == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (source == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (source == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (source == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
+ }\r
+ else if (source == featureSettings)\r
+ {\r
+ new FeatureSettings(alignPanel);\r
+ }\r
+ else if (source == alProperties)\r
+ {\r
+ StringBuffer contents = new jalview.io.AlignmentProperties(\r
+ viewport.alignment).formatAsString();\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ cap.setText(contents.toString());\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "\r
+ + getTitle(), 400, 250);\r
+ }\r
+ else if (source == overviewMenuItem)\r
+ {\r
+ overviewMenuItem_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ changeColour(null);\r
+ }\r
+ else if (source == clustalColour)\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+ else if (source == nucleotideColour)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+ else if (source == modifyPID)\r
+ {\r
+ modifyPID_actionPerformed();\r
+ }\r
+ else if (source == modifyConservation)\r
+ {\r
+ modifyConservation_actionPerformed();\r
+ }\r
+ else if (source == userDefinedColour)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+ else if (source == annotationColour)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+ else if (source == sortPairwiseMenuItem)\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortIDMenuItem)\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortLengthMenuItem)\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortGroupMenuItem)\r
+ {\r
+ sortGroupMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeRedundancyMenuItem)\r
+ {\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ }\r
+ else if (source == pairwiseAlignmentMenuItem)\r
+ {\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ }\r
+ else if (source == PCAMenuItem)\r
+ {\r
+ PCAMenuItem_actionPerformed();\r
+ }\r
+ else if (source == averageDistanceTreeMenuItem)\r
+ {\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == neighbourTreeMenuItem)\r
+ {\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == njTreeBlosumMenuItem)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == avDistanceTreeBlosumMenuItem)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == documentation)\r
+ {\r
+ documentation_actionPerformed();\r
+ }\r
+ else if (source == about)\r
+ {\r
+ about_actionPerformed();\r
+ }\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Alignment output - " + e.getActionCommand(), 600, 500);\r
+ cap.setText(new AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(), viewport.getAlignment(),\r
+ viewport.showJVSuffix));\r
+ }\r
+\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.showAnnotation ? viewport.alignment\r
+ .getAlignmentAnnotation() : null, viewport.alignment\r
+ .getGroups(),\r
+ ((Alignment) viewport.alignment).alignmentProperties);\r
+\r
+ if (displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
+\r
+ return annotation;\r
+ }\r
+\r
+ private Hashtable getDisplayedFeatureCols()\r
+ {\r
+ if (alignPanel.getFeatureRenderer() != null)\r
+ {\r
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
+ Hashtable fcols = new Hashtable();\r
+ Enumeration en = viewport.featuresDisplayed.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ Object col = en.nextElement();\r
+ fcols.put(col, fr.featureColours.get(col));\r
+ }\r
+ return fcols;\r
+ }\r
+ return null;\r
+ }\r
+\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
+ {\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ features = new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
+ }\r
+ else\r
+ {\r
+ features = new FeaturesFile().printGFFFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
+ }\r
+\r
+ if (displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
+\r
+ cap.setText(features);\r
+ }\r
+\r
+ return features;\r
+ }\r
+\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ url.append("?open="\r
+ + appendProtocol(viewport.applet.getParameter("file")));\r
+\r
+ if (viewport.applet.getParameter("features") != null)\r
+ {\r
+ url.append("&features=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("features")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("annotations") != null)\r
+ {\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("jnetfile") != null)\r
+ {\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("defaultColour") != null)\r
+ {\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("defaultColour")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("userDefinedColour") != null)\r
+ {\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("userDefinedColour")));\r
+ }\r
+ if (viewport.applet.getParameter("tree") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("tree")));\r
+ }\r
+ if (viewport.applet.getParameter("treeFile") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("treeFile")));\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
+ }\r
+\r
+ String removeWhiteSpace(String colour)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ {\r
+ sb.append("%20");\r
+ }\r
+ else\r
+ {\r
+ sb.append(colour.charAt(i));\r
+ }\r
+ }\r
+\r
+ return sb.toString();\r
+ }\r
+\r
+ String appendProtocol(String url)\r
+ {\r
+ try\r
+ {\r
+ new URL(url);\r
+ url = URLEncoder.encode(url);\r
+ }\r
+ /*\r
+ * When we finally deprecate 1.1 compatibility, we can start to use\r
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch\r
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -\r
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);\r
+ * ex.printStackTrace(); }\r
+ */\r
+ catch (java.net.MalformedURLException ex)\r
+ {\r
+ url = viewport.applet.getCodeBase() + url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ public void closeMenuItem_actionPerformed()\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
+ {\r
+ System.exit(0);\r
+ }\r
+\r
+ this.dispose();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+\r
+ if (viewport.historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ }\r
+\r
+ if (viewport.redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ }\r
+ }\r
+\r
+ public void addHistoryItem(CommandI command)\r
+ {\r
+ if (command.getSize() > 0)\r
+ {\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.removeAllElements();\r
+ updateEditMenuBar();\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.historyList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI command = (CommandI) viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand(null);\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.redoList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand(null);\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
+ }\r
+\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ // For sequence removal and addition, we need to fire\r
+ // the property change event FROM the viewport where the\r
+ // original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
+ {\r
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ {\r
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (originalSource == null)\r
+ {\r
+ // The original view is closed, we must validate\r
+ // the current view against the closed view first\r
+ if (al != null)\r
+ {\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
+ }\r
+\r
+ originalSource = viewport;\r
+ }\r
+\r
+ return originalSource;\r
+ }\r
+\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.getSequences(null).contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+ if (sg.getSequences(null).contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ synchronized void slideSequences(boolean right, int size)\r
+ {\r
+ Vector sg = new Vector();\r
+ if (viewport.cursorMode)\r
+ {\r
+ sg.addElement(viewport.alignment\r
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() != viewport.alignment\r
+ .getHeight())\r
+ {\r
+ sg = viewport.getSelectionGroup().getSequences(\r
+ viewport.hiddenRepSequences);\r
+ }\r
+\r
+ if (sg.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector invertGroup = new Vector();\r
+\r
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ if (!sg.contains(viewport.alignment.getSequenceAt(i)))\r
+ invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
+ }\r
+\r
+ SequenceI[] seqs1 = new SequenceI[sg.size()];\r
+ for (int i = 0; i < sg.size(); i++)\r
+ seqs1[i] = (SequenceI) sg.elementAt(i);\r
+\r
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+ for (int i = 0; i < invertGroup.size(); i++)\r
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
+\r
+ SlideSequencesCommand ssc;\r
+ if (right)\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
+ size, viewport.getGapCharacter());\r
+ else\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
+ size, viewport.getGapCharacter());\r
+\r
+ int groupAdjustment = 0;\r
+ if (ssc.getGapsInsertedBegin() && right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(size, 0);\r
+ else\r
+ groupAdjustment = size;\r
+ }\r
+ else if (!ssc.getGapsInsertedBegin() && !right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(-size, 0);\r
+ else\r
+ groupAdjustment = -size;\r
+ }\r
+\r
+ if (groupAdjustment != 0)\r
+ {\r
+ viewport.getSelectionGroup().setStartRes(\r
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().setEndRes(\r
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+ }\r
+\r
+ boolean appendHistoryItem = false;\r
+ if (viewport.historyList != null && viewport.historyList.size() > 0\r
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+ {\r
+ appendHistoryItem = ssc\r
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
+ .peek());\r
+ }\r
+\r
+ if (!appendHistoryItem)\r
+ addHistoryItem(ssc);\r
+\r
+ repaint();\r
+ }\r
+\r
+ static StringBuffer copiedSequences;\r
+\r
+ static Vector copiedHiddenColumns;\r
+\r
+ protected void copy_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ copiedSequences = new StringBuffer();\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
+\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
+ if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+ {\r
+ copiedHiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
+ {\r
+ int[] region = (int[]) viewport.getColumnSelection()\r
+ .getHiddenColumns().elementAt(i);\r
+\r
+ copiedHiddenColumns.addElement(new int[]\r
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
+ }\r
+ }\r
+ else\r
+ {\r
+ copiedHiddenColumns = null;\r
+ }\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ // FIND START RES\r
+ // Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ // FIND END RES\r
+ // Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap((ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
+\r
+ copiedSequences.append(seq.getName()\r
+ + "\t"\r
+ + startRes\r
+ + "\t"\r
+ + endRes\r
+ + "\t"\r
+ + seq.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
+ }\r
+\r
+ }\r
+\r
+ protected void pasteNew_actionPerformed()\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ protected void pasteThis_actionPerformed()\r
+ {\r
+ paste(false);\r
+ }\r
+\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+\r
+ if (copiedSequences == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
+ Vector seqs = new Vector();\r
+ while (st.hasMoreElements())\r
+ {\r
+ String name = st.nextToken();\r
+ int start = Integer.parseInt(st.nextToken());\r
+ int end = Integer.parseInt(st.nextToken());\r
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
+ }\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+ String newtitle = new String("Copied sequences");\r
+ if (getTitle().startsWith("Copied sequences"))\r
+ {\r
+ newtitle = getTitle();\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + getTitle());\r
+ }\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+ viewport.applet, newtitle, false);\r
+ if (copiedHiddenColumns != null)\r
+ {\r
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+ {\r
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ else\r
+ {\r
+ addSequences(newSeqs);\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ } // could be anything being pasted in here\r
+\r
+ }\r
+\r
+ void addSequences(SequenceI[] seqs)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(seqs[i]);\r
+ }\r
+\r
+ // !newAlignment\r
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
+ seqs, 0, viewport.alignment.getWidth(), viewport.alignment));\r
+\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.alignment.getSequences());\r
+\r
+ }\r
+\r
+ protected void cut_actionPerformed()\r
+ {\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
+ }\r
+\r
+ protected void delete_actionPerformed()\r
+ {\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
+\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
+ SequenceI[] cut = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ cut[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ /*\r
+ * //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.alignment));\r
+\r
+ viewport.setSelectionGroup(null);\r
+ viewport.alignment.deleteGroup(sg);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ if (viewport.getAlignment().getHeight() < 1)\r
+ {\r
+ this.setVisible(false);\r
+ }\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * group consensus toggled\r
+ * \r
+ */\r
+ protected void showGroupConsensus_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+\r
+ }\r
+\r
+ /**\r
+ * group conservation toggled.\r
+ */\r
+ protected void showGroupConservation_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConservation(showGroupConservation.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showConsensusHistogram_actionPerformed()\r
+ {\r
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showSequenceLogo_actionPerformed()\r
+ {\r
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void applyAutoAnnotationSettings_actionPerformed()\r
+ {\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void makeGrpsFromSelection_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
+ viewport.getSequenceSelection(),\r
+ viewport.getAlignmentView(true).getSequenceStrings(\r
+ viewport.getGapCharacter()),\r
+ viewport.alignment.getGroups());\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
+ viewport.setSelectionGroup(null);\r
+ // set view properties for each group\r
+ for (int g = 0; g < gps.length; g++)\r
+ {\r
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
+ viewport.alignment.addGroup(gps[g]);\r
+ Color col = new Color((int) (Math.random() * 255),\r
+ (int) (Math.random() * 255), (int) (Math.random() * 255));\r
+ col = col.brighter();\r
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
+ .hasMoreElements(); viewport.setSequenceColour(\r
+ (SequenceI) sq.nextElement(), col))\r
+ ;\r
+ }\r
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+ alignPanel.updateAnnotation();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ }\r
+\r
+ protected void deleteGroups_actionPerformed()\r
+ {\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
+ viewport.setSelectionGroup(null);\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
+ viewport.setSelectionGroup(sg);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
+ viewport.setSelectionGroup(null);\r
+ viewport.getColumnSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void invertSequenceMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
+ }\r
+\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void invertColSel_actionPerformed()\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ void trimAlignment(boolean trimLeft)\r
+ {\r
+ ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
+ if (colSel.size() > 0)\r
+ {\r
+ if (trimLeft)\r
+ {\r
+ column = colSel.getMin();\r
+ }\r
+ else\r
+ {\r
+ column = colSel.getMax();\r
+ }\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
+\r
+ TrimRegionCommand trimRegion;\r
+ if (trimLeft)\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT, seqs, column,\r
+ viewport.alignment, viewport.colSel,\r
+ viewport.selectionGroup);\r
+ viewport.setStartRes(0);\r
+ }\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
+ viewport.alignment, viewport.colSel,\r
+ viewport.selectionGroup);\r
+ }\r
+\r
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
+\r
+ addHistoryItem(trimRegion);\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ {\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+ }\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
+ }\r
+ }\r
+\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
+\r
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
+ "Remove Gapped Columns", seqs, start, end, viewport.alignment);\r
+\r
+ addHistoryItem(removeGapCols);\r
+\r
+ statusBar.setText("Removed " + removeGapCols.getSize()\r
+ + " empty columns.");\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
+\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
+\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
+\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
+ viewport.alignment));\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+\r
+ public void findMenuItem_actionPerformed()\r
+ {\r
+ new Finder(alignPanel);\r
+ }\r
+\r
+ /**\r
+ * create a new view derived from the current view\r
+ * \r
+ * @param viewtitle\r
+ * @return frame for the new view\r
+ */\r
+ public AlignFrame newView(String viewtitle)\r
+ {\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows)\r
+ {\r
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
+ .getFullAlignment().getSequencesArray());\r
+ }\r
+ else\r
+ {\r
+ newal = new Alignment(viewport.alignment.getSequencesArray());\r
+ }\r
+\r
+ if (viewport.alignment.getAlignmentAnnotation() != null)\r
+ {\r
+ for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
+\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ viewSize++;\r
+ }\r
+ }\r
+\r
+ String title = new String(this.getTitle());\r
+ if (viewtitle != null)\r
+ {\r
+ title = viewtitle + " ( " + title + ")";\r
+ }\r
+ else\r
+ {\r
+ if (title.indexOf("(View") > -1)\r
+ {\r
+ title = title.substring(0, title.indexOf("(View"));\r
+ }\r
+ title += "(View " + viewSize + ")";\r
+ }\r
+\r
+ newaf.setTitle(title.toString());\r
+\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
+ return newaf;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return list of feature groups on the view\r
+ */\r
+ public String[] getFeatureGroups()\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get sequence feature groups that are hidden or shown\r
+ * \r
+ * @param visible\r
+ * true is visible\r
+ * @return list\r
+ */\r
+ public String[] getFeatureGroupsOfState(boolean visible)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups(visible);\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Change the display state for the given feature groups\r
+ * \r
+ * @param groups\r
+ * list of group strings\r
+ * @param state\r
+ * visible or invisible\r
+ */\r
+ public void setFeatureGroupState(String[] groups, boolean state)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ this.sequenceFeatures.setState(true);\r
+ viewport.showSequenceFeatures(true);\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ fr.setGroupState(groups, state);\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+ }\r
+\r
+ public void seqLimits_itemStateChanged()\r
+ {\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
+ alignPanel.fontChanged();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void colourTextMenuItem_actionPerformed()\r
+ {\r
+ viewport.setColourText(colourTextMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void displayNonconservedMenuItem_actionPerformed()\r
+ {\r
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void wrapMenuItem_actionPerformed()\r
+ {\r
+ viewport.setWrapAlignment(wrapMenuItem.getState());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
+ scaleAbove.setEnabled(wrapMenuItem.getState());\r
+ scaleLeft.setEnabled(wrapMenuItem.getState());\r
+ scaleRight.setEnabled(wrapMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void overviewMenuItem_actionPerformed()\r
+ {\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ OverviewPanel overview = new OverviewPanel(alignPanel);\r
+ frame.add(overview);\r
+ // +50 must allow for applet frame window\r
+ jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
+\r
+ frame.pack();\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ alignPanel.setOverviewPanel(null);\r
+ };\r
+ });\r
+\r
+ alignPanel.setOverviewPanel(overview);\r
+\r
+ }\r
+\r
+ void changeColour(ColourSchemeI cs)\r
+ {\r
+ int threshold = 0;\r
+\r
+ if (cs != null)\r
+ {\r
+ if (viewport.getAbovePIDThreshold())\r
+ {\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
+\r
+ cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+\r
+ viewport.setGlobalColourScheme(cs);\r
+ }\r
+ else\r
+ {\r
+ cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
+ cs, "Background"));\r
+\r
+ }\r
+ else\r
+ {\r
+ cs.setConservation(null);\r
+ }\r
+\r
+ cs.setConsensus(viewport.hconsensus);\r
+\r
+ }\r
+ viewport.setGlobalColourScheme(cs);\r
+\r
+ if (viewport.getColourAppliesToAllGroups())\r
+ {\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+\r
+ if (cs == null)\r
+ {\r
+ sg.cs = null;\r
+ continue;\r
+ }\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ sg.cs = cs;\r
+ }\r
+ }\r
+\r
+ if (viewport.getAbovePIDThreshold()\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
+ {\r
+ sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
+ sg.getWidth()));\r
+ }\r
+ else\r
+ {\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (viewport.getConservationSelected())\r
+ {\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
+ viewport.alignment.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+ sg.cs.setConservation(c);\r
+ }\r
+ else\r
+ {\r
+ sg.cs.setConservation(null);\r
+ sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ if (alignPanel.getOverviewPanel() != null)\r
+ {\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
+ }\r
+\r
+ jalview.structure.StructureSelectionManager\r
+ .getStructureSelectionManager().sequenceColoursChanged(\r
+ alignPanel);\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ protected void modifyPID_actionPerformed()\r
+ {\r
+ if (viewport.getAbovePIDThreshold()\r
+ && viewport.globalColourScheme != null)\r
+ {\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ }\r
+\r
+ protected void modifyConservation_actionPerformed()\r
+ {\r
+ if (viewport.getConservationSelected()\r
+ && viewport.globalColourScheme != null)\r
+ {\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme, "Background");\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ }\r
+\r
+ protected void conservationMenuItem_actionPerformed()\r
+ {\r
+ viewport.setConservationSelected(conservationMenuItem.getState());\r
+\r
+ viewport.setAbovePIDThreshold(false);\r
+ abovePIDThreshold.setState(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyConservation_actionPerformed();\r
+ }\r
+\r
+ public void abovePIDThreshold_actionPerformed()\r
+ {\r
+ viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
+\r
+ conservationMenuItem.setState(false);\r
+ viewport.setConservationSelected(false);\r
+\r
+ changeColour(viewport.getGlobalColourScheme());\r
+\r
+ modifyPID_actionPerformed();\r
+ }\r
+\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
+ .getAlignment().getSequenceAt(0), null);\r
+\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortIDMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortLengthMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByLength(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortGroupMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+\r
+ }\r
+\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
+ {\r
+ new RedundancyPanel(alignPanel);\r
+ }\r
+\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
+ {\r
+ Frame frame = new Frame();\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,\r
+ 500);\r
+ }\r
+ }\r
+\r
+ public void PCAMenuItem_actionPerformed()\r
+ {\r
+ // are the sequences aligned?\r
+ if (!viewport.alignment.isAligned(false))\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ if ((viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() < 4 && viewport\r
+ .getSelectionGroup().getSize() > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ new PCAPanel(viewport);\r
+ } catch (java.lang.OutOfMemoryError ex)\r
+ {\r
+ }\r
+\r
+ }\r
+\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("AV", "PID", "Average distance tree using PID");\r
+ }\r
+\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
+ }\r
+\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
+ }\r
+\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
+ {\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
+ }\r
+\r
+ void NewTreePanel(String type, String pwType, String title)\r
+ {\r
+ // are the sequences aligned?\r
+ if (!viewport.alignment.isAligned(false))\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+\r
+ }\r
+\r
+ if ((viewport.getSelectionGroup() != null && viewport\r
+ .getSelectionGroup().getSize() > 1)\r
+ || (viewport.getSelectionGroup() == null && viewport.alignment\r
+ .getHeight() > 1))\r
+ {\r
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
+\r
+ addTreeMenuItem(tp, title);\r
+\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ }\r
+ }\r
+\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.setTreeImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
+\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+\r
+ /**\r
+ * sort the alignment using the given treePanel\r
+ * \r
+ * @param treePanel\r
+ * tree used to sort view\r
+ * @param title\r
+ * string used for undo event name\r
+ */\r
+ public void sortByTree(TreePanel treePanel, String title)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter\r
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * Do any automatic reordering of the alignment and add the necessary bits to\r
+ * the menu structure for the new tree\r
+ * \r
+ * @param treePanel\r
+ * @param title\r
+ */\r
+ protected void addTreeMenuItem(final TreePanel treePanel,\r
+ final String title)\r
+ {\r
+ final MenuItem item = new MenuItem(title);\r
+ sortByTreeMenu.add(item);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ sortByTree(treePanel, title); // treePanel.getTitle());\r
+ }\r
+ });\r
+\r
+ treePanel.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowOpened(WindowEvent e)\r
+ {\r
+ if (viewport.sortByTree)\r
+ {\r
+ sortByTree(treePanel, title);\r
+ }\r
+ super.windowOpened(e);\r
+ }\r
+\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ sortByTreeMenu.remove(item);\r
+ };\r
+ });\r
+ }\r
+ public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment()\r
+ .getSequencesArray();\r
+ if (viewport.applet.debug)\r
+ {\r
+ System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
+ }\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+ if (undoname!=null)\r
+ {\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ return true;\r
+ }\r
+ protected void documentation_actionPerformed()\r
+ {\r
+ showURL("http://www.jalview.org/help.html", "HELP");\r
+ }\r
+\r
+ protected void about_actionPerformed()\r
+ {\r
+\r
+ class AboutPanel extends Canvas\r
+ {\r
+ String version;\r
+\r
+ String builddate;\r
+\r
+ public AboutPanel(String version, String builddate)\r
+ {\r
+ this.version = version;\r
+ this.builddate = builddate;\r
+ }\r
+\r
+ public void paint(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int fh = fm.getHeight();\r
+ int y = 5, x = 7;\r
+ g.setColor(Color.black);\r
+ // TODO: update this text for each release or centrally store it for\r
+ // lite and application\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
+ g.drawString("JalviewLite - Release " + version, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
+ g.drawString("Build date: " + builddate, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
+ g.drawString(\r
+ "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+ x, y += fh * 1.5);\r
+ g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+ g.drawString(\r
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
+ x, y += fh);\r
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);\r
+ g.drawString(\r
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
+ x, y += fh);\r
+ }\r
+ }\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
+ .getBuildDate()));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
+\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (viewport.applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ if (url.indexOf(":") == -1)\r
+ {\r
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to\r
+ // form valid URL\r
+ // Should really use docbase, not codebase.\r
+ if (url.indexOf("/") == 0)\r
+ {\r
+ String codebase = viewport.applet.getCodeBase().toString();\r
+ url = codebase.substring(0, codebase.length()\r
+ - viewport.applet.getCodeBase().getFile().length())\r
+ + url;\r
+ }\r
+ else\r
+ {\r
+ url = viewport.applet.getCodeBase() + url;\r
+ }\r
+ System.out.println("Show url (prepended codebase): " + url);\r
+ }\r
+ else\r
+ {\r
+ System.out.println("Show url: " + url);\r
+ }\r
+ if (url.indexOf("javascript:") == 0)\r
+ {\r
+ // no target for the javascript context\r
+ viewport.applet.getAppletContext().showDocument(\r
+ new java.net.URL(url));\r
+ }\r
+ else\r
+ {\r
+ viewport.applet.getAppletContext().showDocument(\r
+ new java.net.URL(url), target);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////////////////////////////////////////\r
+ // JBuilder Graphics here\r
+\r
+ MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+ Menu fileMenu = new Menu("File");\r
+\r
+ MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+\r
+ MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+ Menu editMenu = new Menu("Edit");\r
+\r
+ Menu viewMenu = new Menu("View");\r
+\r
+ Menu colourMenu = new Menu("Colour");\r
+\r
+ Menu calculateMenu = new Menu("Calculate");\r
+\r
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+ MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+ MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+ MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+ MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+ MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+ MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+ MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+ MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+ MenuItem PCAMenuItem = new MenuItem();\r
+\r
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+ MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public Label statusBar = new Label();\r
+\r
+ Menu outputTextboxMenu = new Menu();\r
+\r
+ MenuItem clustalColour = new MenuItem();\r
+\r
+ MenuItem zappoColour = new MenuItem();\r
+\r
+ MenuItem taylorColour = new MenuItem();\r
+\r
+ MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+ MenuItem helixColour = new MenuItem();\r
+\r
+ MenuItem strandColour = new MenuItem();\r
+\r
+ MenuItem turnColour = new MenuItem();\r
+\r
+ MenuItem buriedColour = new MenuItem();\r
+\r
+ MenuItem userDefinedColour = new MenuItem();\r
+\r
+ MenuItem PIDColour = new MenuItem();\r
+\r
+ MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+\r
+ MenuItem undoMenuItem = new MenuItem();\r
+\r
+ MenuItem redoMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem findMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+ MenuItem nucleotideColour = new MenuItem();\r
+\r
+ MenuItem deleteGroups = new MenuItem();\r
+\r
+ MenuItem grpsFromSelection = new MenuItem();\r
+\r
+ MenuItem delete = new MenuItem();\r
+\r
+ MenuItem copy = new MenuItem();\r
+\r
+ MenuItem cut = new MenuItem();\r
+\r
+ Menu pasteMenu = new Menu();\r
+\r
+ MenuItem pasteNew = new MenuItem();\r
+\r
+ MenuItem pasteThis = new MenuItem();\r
+\r
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+\r
+ MenuItem font = new MenuItem();\r
+\r
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
+ MenuItem modifyPID = new MenuItem();\r
+\r
+ MenuItem modifyConservation = new MenuItem();\r
+\r
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
+ "Autocalculate Consensus", true);\r
+\r
+ Menu sortByTreeMenu = new Menu();\r
+\r
+ Menu sort = new Menu();\r
+\r
+ Menu calculate = new Menu();\r
+\r
+ MenuItem inputText = new MenuItem();\r
+\r
+ Menu helpMenu = new Menu();\r
+\r
+ MenuItem documentation = new MenuItem();\r
+\r
+ MenuItem about = new MenuItem();\r
+\r
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
+ \r
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
+ Menu autoAnnMenu=new Menu();\r
+ CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+\r
+ item = new MenuItem(\r
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
+\r
+ loadTree.addActionListener(this);\r
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortLengthMenuItem.setLabel("by Length");\r
+ sortLengthMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem\r
+ .setLabel("Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem\r
+ .setLabel("Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ displayNonconservedMenuItem.setLabel("Show nonconserved");\r
+ displayNonconservedMenuItem.addItemListener(this);\r
+ alProperties.addActionListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ grpsFromSelection.setLabel("Make Groups for selection");\r
+ grpsFromSelection.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\r
+ font.addActionListener(this);\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+ centreColumnLabelFlag.setLabel("Centre column labels");\r
+ centreColumnLabelFlag.addItemListener(this);\r
+ followMouseOverFlag.setLabel("Automatic Scrolling");\r
+ followMouseOverFlag.addItemListener(this);\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\r
+ invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+ invertColSel.setLabel("Invert Column Selection");\r
+ menu1.setLabel("Show");\r
+ showColumns.setLabel("All Columns ");\r
+ showSeqs.setLabel("All Sequences");\r
+ menu2.setLabel("Hide");\r
+ hideColumns.setLabel("Selected Columns");\r
+ hideSequences.setLabel("Selected Sequences");\r
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");\r
+ hideAllSelection.setLabel("Selected Region");\r
+ showAllHidden.setLabel("All Sequences and Columns");\r
+ showGroupConsensus.setLabel("Group Consensus");\r
+ showGroupConservation.setLabel("Group Conservation");\r
+ showConsensusHistogram.setLabel("Show Consensus Histogram");\r
+ showSequenceLogo.setLabel("Show Consensus Logo");\r
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
+ applyAutoAnnotationSettings.setState(true);\r
+ autoAnnMenu.setLabel("Autocalculated Annotation");\r
+ \r
+ invertColSel.addActionListener(this);\r
+ showColumns.addActionListener(this);\r
+ showSeqs.addActionListener(this);\r
+ hideColumns.addActionListener(this);\r
+ hideSequences.addActionListener(this);\r
+ hideAllButSelection.addActionListener(this);\r
+ hideAllSelection.addActionListener(this);\r
+ showAllHidden.addActionListener(this);\r
+ showGroupConsensus.addItemListener(this);\r
+ showGroupConservation.addItemListener(this);\r
+ showConsensusHistogram.addItemListener(this);\r
+ showSequenceLogo.addItemListener(this);\r
+ applyAutoAnnotationSettings.addItemListener(this);\r
+ formatMenu.setLabel("Format");\r
+ selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
+ if (jalviewServletURL != null)\r
+ {\r
+ fileMenu.add(loadApplication);\r
+ }\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(followMouseOverFlag);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ autoAnnMenu.add(applyAutoAnnotationSettings);\r
+ autoAnnMenu.add(showConsensusHistogram);\r
+ autoAnnMenu.add(showSequenceLogo);\r
+ autoAnnMenu.addSeparator();\r
+ autoAnnMenu.add(showGroupConservation);\r
+ autoAnnMenu.add(showGroupConsensus);\r
+ viewMenu.add(autoAnnMenu);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(alProperties);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortLengthMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ menu1.add(showColumns);\r
+ menu1.add(showSeqs);\r
+ menu1.add(showAllHidden);\r
+ menu2.add(hideColumns);\r
+ menu2.add(hideSequences);\r
+ menu2.add(hideAllSelection);\r
+ menu2.add(hideAllButSelection);\r
+ formatMenu.add(font);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(displayNonconservedMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ formatMenu.add(centreColumnLabelFlag);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(grpsFromSelection);\r
+ selectMenu.add(deleteGroups);\r
+\r
+ }\r
+\r
+ MenuItem featureSettings = new MenuItem();\r
+\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+\r
+ MenuItem annotationColour = new MenuItem();\r
+\r
+ MenuItem invertColSel = new MenuItem();\r
+\r
+ Menu menu1 = new Menu();\r
+\r
+ MenuItem showColumns = new MenuItem();\r
+\r
+ MenuItem showSeqs = new MenuItem();\r
+\r
+ Menu menu2 = new Menu();\r
+\r
+ MenuItem hideColumns = new MenuItem();\r
+\r
+ MenuItem hideSequences = new MenuItem();\r
+\r
+ MenuItem hideAllButSelection = new MenuItem();\r
+\r
+ MenuItem hideAllSelection = new MenuItem();\r
+\r
+ MenuItem showAllHidden = new MenuItem();\r
+\r
+ Menu formatMenu = new Menu();\r
+\r
+ Menu selectMenu = new Menu();\r
+\r
+ MenuItem newView = new MenuItem();\r
+\r
+ /**\r
+ * Attach the alignFrame panels after embedding menus, if necessary. This used\r
+ * to be called setEmbedded, but is now creates the dropdown menus in a\r
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.\r
+ * \r
+ * @param reallyEmbedded\r
+ * true to attach the view to the applet area on the page rather than\r
+ * in a new window\r
+ */\r
+ public void createAlignFrameWindow(boolean reallyEmbedded, String title)\r
+ {\r
+ if (reallyEmbedded)\r
+ {\r
+ // ////\r
+ // Explicly build the embedded menu panel for the on-page applet\r
+ //\r
+ // view cannot be closed if its actually on the page\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Remove Seperator\r
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",\r
+ Font.PLAIN, 10, false); // use our own fonts.\r
+ // and actually add the components to the applet area\r
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+ alignPanel.setSize(viewport.applet.getSize().width,\r
+ viewport.applet.getSize().height - embeddedMenu.HEIGHT\r
+ - statusBar.HEIGHT);\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ final AlignFrame me = this;\r
+ viewport.applet.addFocusListener(new FocusListener()\r
+ {\r
+ \r
+ @Override\r
+ public void focusLost(FocusEvent e)\r
+ {\r
+ if (me.viewport.applet.currentAlignFrame==me) {\r
+ me.viewport.applet.currentAlignFrame = null;\r
+ }}\r
+ \r
+ @Override\r
+ public void focusGained(FocusEvent e)\r
+ {\r
+ me.viewport.applet.currentAlignFrame = me;\r
+ }\r
+ });\r
+ viewport.applet.validate();\r
+ }\r
+ else\r
+ {\r
+ // //////\r
+ // test and embed menu bar if necessary.\r
+ //\r
+ if (embedMenuIfNeeded(alignPanel))\r
+ {\r
+ // adjust for status bar height too\r
+ alignPanel.setSize(getSize().width, getSize().height\r
+ - statusBar.HEIGHT);\r
+ }\r
+ add(statusBar, BorderLayout.SOUTH);\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ // and register with the applet so it can pass external API calls to us\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * create a new binding between structures in an existing jmol viewer instance\r
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,\r
+ * this does not open a new Jmol window, or modify the display of the\r
+ * structures in the original jmol window. Note This method doesn't work\r
+ * without an additional javascript library to exchange messages between the\r
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621\r
+ * \r
+ * @param viewer\r
+ * JmolViewer instance\r
+ * @param sequenceIds\r
+ * - sequence Ids to search for associations\r
+ */\r
+ public SequenceStructureBinding addStructureViewInstance(\r
+ Object jmolviewer, String[] sequenceIds)\r
+ {\r
+ org.jmol.api.JmolViewer viewer = null;\r
+ try\r
+ {\r
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;\r
+ } catch (ClassCastException ex)\r
+ {\r
+ System.err.println("Unsupported viewer object :"\r
+ + jmolviewer.getClass());\r
+ }\r
+ if (viewer == null)\r
+ {\r
+ System.err.println("Can't use this object as a structure viewer:"\r
+ + jmolviewer.getClass());\r
+ return null;\r
+ }\r
+ SequenceI[] seqs = null;\r
+ if (sequenceIds == null || sequenceIds.length == 0)\r
+ {\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ Vector sqi = new Vector();\r
+ AlignmentI al = viewport.getAlignment();\r
+ for (int sid = 0; sid < sequenceIds.length; sid++)\r
+ {\r
+ SequenceI sq = al.findName(sequenceIds[sid]);\r
+ if (sq != null)\r
+ {\r
+ sqi.addElement(sq);\r
+ }\r
+ }\r
+ if (sqi.size() > 0)\r
+ {\r
+ seqs = new SequenceI[sqi.size()];\r
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)\r
+ {\r
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+ ExtJmol jmv = null;\r
+ // TODO: search for a jmv that involves viewer\r
+ if (jmv == null)\r
+ { // create a new viewer/jalview binding.\r
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
+ }\r
+ return jmv;\r
+\r
+ }\r
+ /**\r
+ * bind a pdb file to a sequence in the current view\r
+ * \r
+ * @param sequenceId\r
+ * - sequenceId within the dataset.\r
+ * @param pdbEntryString\r
+ * - the short name for the PDB file\r
+ * @param pdbFile\r
+ * - pdb file - either a URL or a valid PDB file.\r
+ * @return true if binding was as success TODO: consider making an exception\r
+ * structure for indicating when PDB parsing or sequenceId location\r
+ * fails.\r
+ */\r
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,\r
+ String pdbFile)\r
+ {\r
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);\r
+ boolean needtoadd = false;\r
+ if (toaddpdb != null)\r
+ {\r
+ Vector pdbe = toaddpdb.getPDBId();\r
+ PDBEntry pdbentry = null;\r
+ if (pdbe != null && pdbe.size() > 0)\r
+ {\r
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)\r
+ {\r
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);\r
+ if (!pdbentry.getId().equals(pdbEntryString)\r
+ && !pdbentry.getFile().equals(pdbFile))\r
+ {\r
+ pdbentry = null;\r
+ }\r
+ else\r
+ {\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ if (pdbentry == null)\r
+ {\r
+ pdbentry = new PDBEntry();\r
+ pdbentry.setId(pdbEntryString);\r
+ pdbentry.setFile(pdbFile);\r
+ needtoadd = true; // add this new entry to sequence.\r
+ }\r
+ // resolve data source\r
+ // TODO: this code should be a refactored to an io package\r
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");\r
+ if (protocol == null)\r
+ {\r
+ return false;\r
+ }\r
+ if (needtoadd)\r
+ {\r
+ // make a note of the access mode and add\r
+ if (pdbentry.getProperty() == null)\r
+ {\r
+ pdbentry.setProperty(new Hashtable());\r
+ }\r
+ pdbentry.getProperty().put("protocol", protocol);\r
+ toaddpdb.addPDBId(pdbentry);\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+\r
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)\r
+ {\r
+ if (seqs != null)\r
+ {\r
+ Vector sequences = new Vector();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i] != null)\r
+ {\r
+ sequences.addElement(new Object[]\r
+ { seqs[i], (chains != null) ? chains[i] : null });\r
+ }\r
+ }\r
+ seqs = new SequenceI[sequences.size()];\r
+ chains = new String[sequences.size()];\r
+ for (int i = 0, isize = sequences.size(); i < isize; i++)\r
+ {\r
+ Object[] oj = (Object[]) sequences.elementAt(i);\r
+\r
+ seqs[i] = (SequenceI) oj[0];\r
+ chains[i] = (String) oj[1];\r
+ }\r
+ }\r
+ return new Object[]\r
+ { seqs, chains };\r
+\r
+ }\r
+\r
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,\r
+ SequenceI[] seqs, String[] chains, String protocol)\r
+ {\r
+ // Scrub any null sequences from the array\r
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);\r
+ seqs = (SequenceI[]) sqch[0];\r
+ chains = (String[]) sqch[1];\r
+ if (seqs == null || seqs.length == 0)\r
+ {\r
+ System.err\r
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");\r
+ }\r
+ if (protocol == null || protocol.trim().length() == 0\r
+ || protocol.equals("null"))\r
+ {\r
+ protocol = (String) pdb.getProperty().get("protocol");\r
+ if (protocol == null)\r
+ {\r
+ System.err.println("Couldn't work out protocol to open structure: "\r
+ + pdb.getId());\r
+ return;\r
+ }\r
+ }\r
+ if (applet.useXtrnalSviewer)\r
+ {\r
+ // register the association(s) and quit, don't create any windows.\r
+ if (StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
+ System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
+ }\r
+ return;\r
+ }\r
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)\r
+ {\r
+ // can only do alignments with Jmol\r
+ // find the last jmol window assigned to this alignment\r
+ jalview.appletgui.AppletJmol ajm = null, tajm;\r
+ Vector jmols = applet\r
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);\r
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)\r
+ {\r
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);\r
+ if (tajm.ap.alignFrame == this)\r
+ {\r
+ ajm = tajm;\r
+ break;\r
+ }\r
+ }\r
+ if (ajm != null)\r
+ {\r
+ System.err\r
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");\r
+ // try and add the pdb structure\r
+ // ajm.addS\r
+ ajm = null;\r
+ }\r
+ }\r
+ // otherwise, create a new window\r
+ if (applet.jmolAvailable)\r
+ {\r
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,\r
+ protocol);\r
+ applet.lastFrameX += 40;\r
+ applet.lastFrameY += 40;\r
+ }\r
+ else\r
+ {\r
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);\r
+ }\r
+\r
+ }\r
+\r
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,\r
+ SequenceI[][] seqs, String[][] chains, String[] protocols)\r
+ {\r
+ // TODO Auto-generated method stub\r
+ System.err.println("Aligned Structure View: Not yet implemented.");\r
+ }\r
+\r
+ /**\r
+ * modify the current selection, providing the user has not made a selection already.\r
+ * @param sel - sequences from this alignment \r
+ * @param csel - columns to be selected on the alignment\r
+ */\r
+ public void select(SequenceGroup sel, ColumnSelection csel)\r
+ {\r
+ alignPanel.seqPanel.selection(sel, csel, null);\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff