From fa93bb578999b13c0364a712ae368ca8841012a1 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 2 May 2007 12:24:41 +0000 Subject: [PATCH] refactored do and undo() method to take array of alignments for operations that result in hide/show of alignment annotation --- src/jalview/appletgui/AlignFrame.java | 5781 +++++++++++------------ src/jalview/appletgui/RedundancyPanel.java | 644 +-- src/jalview/commands/ChangeCaseCommand.java | 266 +- src/jalview/commands/CommandI.java | 60 +- src/jalview/commands/EditCommand.java | 133 +- src/jalview/commands/OrderCommand.java | 124 +- src/jalview/commands/RemoveGapColCommand.java | 212 +- src/jalview/commands/RemoveGapsCommand.java | 240 +- src/jalview/commands/SlideSequencesCommand.java | 186 +- src/jalview/commands/TrimRegionCommand.java | 356 +- src/jalview/gui/RedundancyPanel.java | 670 +-- 11 files changed, 4381 insertions(+), 4291 deletions(-) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 12a2938..e17af38 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,2891 +1,2890 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.io.*; -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; - -public class AlignFrame - extends Frame implements ActionListener, - ItemListener, KeyListener, MouseListener -{ - 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); - - 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(); - } - } - - param = applet.getParameter("wrap"); - if (param != null) - { - if (param.equalsIgnoreCase("true")) - { - wrapMenuItem.setState(true); - wrapMenuItem_actionPerformed(); - } - } - - 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); - - if (embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } - alignPanel.validate(); - alignPanel.paintAlignment(true); - } - - public AlignViewport getAlignViewport() - { - return viewport; - } - - 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); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - if (featuresFile) - { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureLinks = featureLinks; - } - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - 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(); - 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(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - - 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(); - } - } - break; - } - - case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(true); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - - viewport.endSeq + viewport.startSeq); - } - break; - - case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } - break; - - case KeyEvent.VK_Z: - if (evt.isControlDown()) - { - undoMenuItem_actionPerformed(); - } - break; - - case KeyEvent.VK_Y: - if (evt.isControlDown()) - { - redoMenuItem_actionPerformed(); - } - break; - - case KeyEvent.VK_L: - if (evt.isControlDown()) - { - trimAlignment(true); - } - break; - - case KeyEvent.VK_R: - if (evt.isControlDown()) - { - trimAlignment(false); - } - break; - - case KeyEvent.VK_E: - if (evt.isControlDown()) - { - if (evt.isShiftDown()) - { - this.removeAllGapsMenuItem_actionPerformed(); - } - else - { - removeGappedColumnMenuItem_actionPerformed(); - } - } - break; - case KeyEvent.VK_I: - if (evt.isControlDown()) - { - if (evt.isAltDown()) - { - viewport.invertColumnSelection(); - } - else - { - this.invertSequenceMenuItem_actionPerformed(); - } - } - break; - - case KeyEvent.VK_U: - if (evt.isControlDown()) - { - this.deleteGroups_actionPerformed(); - } - break; - - case KeyEvent.VK_T: - if (evt.isControlDown()) - { - newView(); - } - break; - - } - alignPanel.paintAlignment(true); - } - - public void keyReleased(KeyEvent evt) - {} - - public void keyTyped(KeyEvent evt) - {} - - public void itemStateChanged(ItemEvent evt) - { - if (evt.getSource() == colourTextMenuItem) - { - colourTextMenuItem_actionPerformed(); - } - else if (evt.getSource() == wrapMenuItem) - { - wrapMenuItem_actionPerformed(); - } - else if (evt.getSource() == scaleAbove) - { - 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(); - } - - alignPanel.paintAlignment(true); - } - - 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 == 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(); - } - else if (source == showColumns) - { - viewport.showAllHiddenColumns(); - alignPanel.paintAlignment(true); - } - else if (source == showSeqs) - { - viewport.showAllHiddenSeqs(); - } - else if (source == hideColumns) - { - viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); - } - else if (source == hideSequences && viewport.getSelectionGroup() != null) - { - viewport.hideAllSelectedSeqs(); - } - else if (source == featureSettings) - { - new FeatureSettings(alignPanel); - } - else if(source== alProperties) - { - StringBuffer contents = new StringBuffer(); - - float avg = 0; - int min=Integer.MAX_VALUE, max=0; - for(int i=0; imax) - max = size; - if(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(); - - 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(); - - 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); - } - } - - 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()); - } - - 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()); - } - - 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()); - } - - 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); - } - - public void newView() - { - 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 (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; - - } - - 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 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)); - addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); - } - - public void sortIDMenuItem_actionPerformed() - { - // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - // HistoryItem.SORT)); - AlignmentSorter.sortByID(viewport.getAlignment()); - alignPanel.paintAlignment(true); - } - - public void sortGroupMenuItem_actionPerformed() - { - // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - // HistoryItem.SORT)); - AlignmentSorter.sortByGroup(viewport.getAlignment()); - 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()) - { - 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()) - { - 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(viewport, - 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(viewport, - treeFile, - "From File - ", - tree); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); - } - - void addTreeMenuItem(final TreePanel treePanel, String title) - { - final MenuItem item = new MenuItem(title); - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - // addHistoryItem(new HistoryItem("Sort", viewport.alignment, - // HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.paintAlignment(true); - } - }); - - treePanel.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - sortByTreeMenu.remove(item); - }; - }); - } - - protected void documentation_actionPerformed() - { - showURL("http://www.jalview.org/help.html", "HELP"); - } - - protected void about_actionPerformed() - { - - class AboutPanel - extends Canvas - { - String version; - public AboutPanel(String version) - { - this.version = version; - } - - 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); - g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release " + version, 200, y += fh); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", - x, y += fh * 2); - g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", - x, y += fh); - g.drawString( - "For any issues relating to Jalview, email help@jalview.org", x, - y += fh); - g.drawString("If you use JalView, please cite:", x, y += fh + 8); - g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", - x, y += fh); - g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); - } - } - - String version = "test"; - java.net.URL url = getClass().getResource("/.build_properties"); - if (url != null) - { - try - { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); - String line; - while ( (line = reader.readLine()) != null) - { - if (line.indexOf("VERSION") > -1) - { - version = line.substring(line.indexOf("=") + 1); - } - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - Frame frame = new Frame(); - frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); - - } - - public void showURL(String url, String target) - { - if (viewport.applet == null) - { - System.out.println("Not running as applet - no browser available."); - } - else - { - try - { - System.out.println("Show url: " + url); - viewport.applet.getAppletContext().showDocument(new java.net.URL(url), - target); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - ////////////////////////////////////////////////////////////////////////////////// - //JBuilder Graphics here - - MenuBar alignFrameMenuBar = new MenuBar(); - Menu fileMenu = new Menu("File"); - MenuItem loadApplication = new MenuItem("View in Full Application"); - MenuItem loadTree = new MenuItem("Load Associated Tree ..."); - MenuItem loadAnnotations = new MenuItem( - "Load Features/Annotations ..."); - MenuItem outputFeatures = new MenuItem("Export Features ..."); - MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); - - MenuItem closeMenuItem = new MenuItem("Close"); - Menu editMenu = new Menu("Edit"); - Menu viewMenu = new Menu("View"); - Menu colourMenu = new Menu("Colour"); - Menu calculateMenu = new Menu("Calculate"); - MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - MenuItem remove2LeftMenuItem = new MenuItem(); - MenuItem remove2RightMenuItem = new MenuItem(); - MenuItem removeGappedColumnMenuItem = new MenuItem(); - MenuItem removeAllGapsMenuItem = new MenuItem(); - CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - MenuItem sortPairwiseMenuItem = new MenuItem(); - MenuItem sortIDMenuItem = new MenuItem(); - MenuItem sortGroupMenuItem = new MenuItem(); - MenuItem removeRedundancyMenuItem = new MenuItem(); - MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - MenuItem PCAMenuItem = new MenuItem(); - MenuItem averageDistanceTreeMenuItem = new MenuItem(); - MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - Menu outputTextboxMenu = new Menu(); - MenuItem clustalColour = new MenuItem(); - MenuItem zappoColour = new MenuItem(); - MenuItem taylorColour = new MenuItem(); - MenuItem hydrophobicityColour = new MenuItem(); - MenuItem helixColour = new MenuItem(); - MenuItem strandColour = new MenuItem(); - MenuItem turnColour = new MenuItem(); - MenuItem buriedColour = new MenuItem(); - MenuItem userDefinedColour = new MenuItem(); - MenuItem PIDColour = new MenuItem(); - MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem alProperties = new MenuItem("Alignment Properties..."); - MenuItem overviewMenuItem = new MenuItem(); - MenuItem undoMenuItem = new MenuItem(); - MenuItem redoMenuItem = new MenuItem(); - CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu pasteMenu = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - MenuItem font = new MenuItem(); - CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - Panel embeddedMenu; - Label embeddedEdit; - Label embeddedSelect; - Label embeddedView; - Label embeddedFormat; - Label embeddedColour; - Label embeddedFile; - Label embeddedHelp; - Label embeddedCalculate; - FlowLayout flowLayout1; - - 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); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(this); - alProperties.addActionListener(this); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(this); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(this); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(this); - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); - seqLimits.setLabel("Show Sequence Limits"); - seqLimits.addItemListener(this); - featureSettings.setLabel("Feature Settings..."); - 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"); - invertColSel.addActionListener(this); - showColumns.addActionListener(this); - showSeqs.addActionListener(this); - hideColumns.addActionListener(this); - hideSequences.addActionListener(this); - formatMenu.setLabel("Format"); - selectMenu.setLabel("Select"); - newView.setLabel("New View"); - newView.addActionListener(this); - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(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(annotationPanelMenuItem); - 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(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - menu1.add(showColumns); - menu1.add(showSeqs); - menu2.add(hideColumns); - menu2.add(hideSequences); - formatMenu.add(font); - formatMenu.add(seqLimits); - formatMenu.add(wrapMenuItem); - formatMenu.add(scaleAbove); - formatMenu.add(scaleLeft); - formatMenu.add(scaleRight); - formatMenu.add(viewBoxesMenuItem); - formatMenu.add(viewTextMenuItem); - formatMenu.add(colourTextMenuItem); - formatMenu.add(renderGapsMenuItem); - selectMenu.add(findMenuItem); - selectMenu.addSeparator(); - selectMenu.add(selectAllSequenceMenuItem); - selectMenu.add(deselectAllSequenceMenuItem); - selectMenu.add(invertSequenceMenuItem); - selectMenu.add(invertColSel); - selectMenu.add(deleteGroups); - } - - public void setEmbedded() - { - - embeddedMenu = new Panel(); - embeddedEdit = new Label("Edit"); - embeddedSelect = new Label("Select"); - embeddedView = new Label("View"); - embeddedFormat = new Label("Format"); - embeddedColour = new Label("Colour"); - embeddedFile = new Label("File"); - embeddedHelp = new Label("Help"); - embeddedCalculate = new Label("Calculate"); - flowLayout1 = new FlowLayout(); - embeddedMenu.setBackground(Color.lightGray); - embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedMenu.add(embeddedFile); - embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSelect); - embeddedMenu.add(embeddedView); - embeddedMenu.add(embeddedFormat); - embeddedMenu.add(embeddedColour); - embeddedMenu.add(embeddedCalculate); - embeddedMenu.add(embeddedHelp); - flowLayout1.setAlignment(FlowLayout.LEFT); - flowLayout1.setHgap(2); - flowLayout1.setVgap(0); - embeddedFile.addMouseListener(this); - embeddedEdit.addMouseListener(this); - embeddedSelect.addMouseListener(this); - embeddedView.addMouseListener(this); - embeddedFormat.addMouseListener(this); - embeddedColour.addMouseListener(this); - embeddedCalculate.addMouseListener(this); - embeddedHelp.addMouseListener(this); - - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Seperator - - 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); - viewport.applet.validate(); - - } - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; - MenuItem featureSettings = new MenuItem(); - CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); - MenuItem annotationColour = new MenuItem(); - MenuItem invertColSel = new MenuItem(); - Menu menu1 = new Menu(); - MenuItem showColumns = new MenuItem(); - MenuItem showSeqs = new MenuItem(); - Menu menu2 = new Menu(); - MenuItem hideColumns = new MenuItem(); - MenuItem hideSequences = new MenuItem(); - Menu formatMenu = new Menu(); - Menu selectMenu = new Menu(); - MenuItem newView = new MenuItem(); - - public void mousePressed(MouseEvent evt) - { - PopupMenu popup = null; - Label source = (Label) evt.getSource(); - if (source == embeddedFile) - { - popup = filePopup = genPopupMenu(filePopup, fileMenu); - } - else if (source == embeddedEdit) - { - popup = editPopup = genPopupMenu(editPopup, editMenu); - } - else if (source == embeddedSelect) - { - popup = searchPopup = genPopupMenu(searchPopup, selectMenu); - } - else if (source == embeddedView) - { - popup = viewPopup = genPopupMenu(viewPopup, viewMenu); - } - else if (source == embeddedFormat) - { - popup = formatPopup = genPopupMenu(formatPopup, formatMenu); - } - else if (source == embeddedColour) - { - popup = colourPopup = genPopupMenu(colourPopup, colourMenu); - } - else if (source == embeddedCalculate) - { - popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); - } - else if (source == embeddedHelp) - { - popup = helpPopup = genPopupMenu(helpPopup, helpMenu); - } - - embeddedMenu.add(popup); - popup.show(embeddedMenu, - source.getBounds().x, - source.getBounds().y + source.getBounds().getSize().height); - } - - PopupMenu genPopupMenu(PopupMenu popup, Menu original) - { - if (popup != null) - { - return popup; - } - popup = new PopupMenu(); - int m, mSize = original.getItemCount(); - for (m = 0; m < mSize; m++) - { - popup.add(original.getItem(m)); - mSize--; - m--; - } - - return popup; - } - - public void mouseClicked(MouseEvent evt) - {} - - public void mouseReleased(MouseEvent evt) - {} - - public void mouseEntered(MouseEvent evt) - {} - - public void mouseExited(MouseEvent evt) - {} - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +package jalview.appletgui; + +import java.io.*; +import java.net.*; +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; + +public class AlignFrame + extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener +{ + 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); + + 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(); + } + } + + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) + { + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); + } + } + + 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); + + if (embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + alignPanel.validate(); + alignPanel.paintAlignment(true); + } + + public AlignViewport getAlignViewport() + { + return viewport; + } + + 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); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + if (featuresFile) + { + if (featureLinks.size() > 0) + { + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + } + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + 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(); + 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(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + 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(); + } + } + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + { + this.removeAllGapsMenuItem_actionPerformed(); + } + else + { + removeGappedColumnMenuItem_actionPerformed(); + } + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) + { + viewport.invertColumnSelection(); + } + else + { + this.invertSequenceMenuItem_actionPerformed(); + } + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; + + } + alignPanel.paintAlignment(true); + } + + public void keyReleased(KeyEvent evt) + {} + + public void keyTyped(KeyEvent evt) + {} + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == colourTextMenuItem) + { + colourTextMenuItem_actionPerformed(); + } + else if (evt.getSource() == wrapMenuItem) + { + wrapMenuItem_actionPerformed(); + } + else if (evt.getSource() == scaleAbove) + { + 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(); + } + + alignPanel.paintAlignment(true); + } + + 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 == 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(); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == hideSequences && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + } + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if(source== alProperties) + { + StringBuffer contents = new StringBuffer(); + + float avg = 0; + int min=Integer.MAX_VALUE, max=0; + for(int i=0; imax) + max = size; + if(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); + } + } + + 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()); + } + + 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()); + } + + 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()); + } + + 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); + } + + public void newView() + { + 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 (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; + + } + + 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 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)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortIDMenuItem_actionPerformed() + { + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); + AlignmentSorter.sortByID(viewport.getAlignment()); + alignPanel.paintAlignment(true); + } + + public void sortGroupMenuItem_actionPerformed() + { + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + 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()) + { + 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()) + { + 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(viewport, + 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(viewport, + treeFile, + "From File - ", + tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); + } + + void addTreeMenuItem(final TreePanel treePanel, String title) + { + final MenuItem item = new MenuItem(title); + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); + AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); + alignPanel.paintAlignment(true); + } + }); + + treePanel.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent e) + { + sortByTreeMenu.remove(item); + }; + }); + } + + protected void documentation_actionPerformed() + { + showURL("http://www.jalview.org/help.html", "HELP"); + } + + protected void about_actionPerformed() + { + + class AboutPanel + extends Canvas + { + String version; + public AboutPanel(String version) + { + this.version = version; + } + + 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); + g.setFont(new Font("Helvetica", Font.BOLD, 14)); + g.drawString("Jalview - Release " + version, 200, y += fh); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", + x, y += fh * 2); + g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", + x, y += fh); + g.drawString( + "For any issues relating to Jalview, email help@jalview.org", x, + y += fh); + g.drawString("If you use JalView, please cite:", x, y += fh + 8); + g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", + x, y += fh); + g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); + } + } + + String version = "test"; + java.net.URL url = getClass().getResource("/.build_properties"); + if (url != null) + { + try + { + BufferedReader reader = new BufferedReader(new InputStreamReader( + url.openStream())); + String line; + while ( (line = reader.readLine()) != null) + { + if (line.indexOf("VERSION") > -1) + { + version = line.substring(line.indexOf("=") + 1); + } + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + Frame frame = new Frame(); + frame.add(new AboutPanel(version)); + jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); + + } + + public void showURL(String url, String target) + { + if (viewport.applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + System.out.println("Show url: " + url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), + target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + ////////////////////////////////////////////////////////////////////////////////// + //JBuilder Graphics here + + MenuBar alignFrameMenuBar = new MenuBar(); + Menu fileMenu = new Menu("File"); + MenuItem loadApplication = new MenuItem("View in Full Application"); + MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + MenuItem loadAnnotations = new MenuItem( + "Load Features/Annotations ..."); + MenuItem outputFeatures = new MenuItem("Export Features ..."); + MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + MenuItem closeMenuItem = new MenuItem("Close"); + Menu editMenu = new Menu("Edit"); + Menu viewMenu = new Menu("View"); + Menu colourMenu = new Menu("Colour"); + Menu calculateMenu = new Menu("Calculate"); + MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + MenuItem remove2LeftMenuItem = new MenuItem(); + MenuItem remove2RightMenuItem = new MenuItem(); + MenuItem removeGappedColumnMenuItem = new MenuItem(); + MenuItem removeAllGapsMenuItem = new MenuItem(); + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + MenuItem sortPairwiseMenuItem = new MenuItem(); + MenuItem sortIDMenuItem = new MenuItem(); + MenuItem sortGroupMenuItem = new MenuItem(); + MenuItem removeRedundancyMenuItem = new MenuItem(); + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + MenuItem PCAMenuItem = new MenuItem(); + MenuItem averageDistanceTreeMenuItem = new MenuItem(); + MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + Menu outputTextboxMenu = new Menu(); + MenuItem clustalColour = new MenuItem(); + MenuItem zappoColour = new MenuItem(); + MenuItem taylorColour = new MenuItem(); + MenuItem hydrophobicityColour = new MenuItem(); + MenuItem helixColour = new MenuItem(); + MenuItem strandColour = new MenuItem(); + MenuItem turnColour = new MenuItem(); + MenuItem buriedColour = new MenuItem(); + MenuItem userDefinedColour = new MenuItem(); + MenuItem PIDColour = new MenuItem(); + MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem alProperties = new MenuItem("Alignment Properties..."); + MenuItem overviewMenuItem = new MenuItem(); + MenuItem undoMenuItem = new MenuItem(); + MenuItem redoMenuItem = new MenuItem(); + CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + MenuItem font = new MenuItem(); + CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + Panel embeddedMenu; + Label embeddedEdit; + Label embeddedSelect; + Label embeddedView; + Label embeddedFormat; + Label embeddedColour; + Label embeddedFile; + Label embeddedHelp; + Label embeddedCalculate; + FlowLayout flowLayout1; + + 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); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + alProperties.addActionListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + 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"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(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(annotationPanelMenuItem); + 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(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); + } + + public void setEmbedded() + { + + embeddedMenu = new Panel(); + embeddedEdit = new Label("Edit"); + embeddedSelect = new Label("Select"); + embeddedView = new Label("View"); + embeddedFormat = new Label("Format"); + embeddedColour = new Label("Colour"); + embeddedFile = new Label("File"); + embeddedHelp = new Label("Help"); + embeddedCalculate = new Label("Calculate"); + flowLayout1 = new FlowLayout(); + embeddedMenu.setBackground(Color.lightGray); + embeddedMenu.setLayout(flowLayout1); + embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedMenu.add(embeddedFile); + embeddedMenu.add(embeddedEdit); + embeddedMenu.add(embeddedSelect); + embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedFormat); + embeddedMenu.add(embeddedColour); + embeddedMenu.add(embeddedCalculate); + embeddedMenu.add(embeddedHelp); + flowLayout1.setAlignment(FlowLayout.LEFT); + flowLayout1.setHgap(2); + flowLayout1.setVgap(0); + embeddedFile.addMouseListener(this); + embeddedEdit.addMouseListener(this); + embeddedSelect.addMouseListener(this); + embeddedView.addMouseListener(this); + embeddedFormat.addMouseListener(this); + embeddedColour.addMouseListener(this); + embeddedCalculate.addMouseListener(this); + embeddedHelp.addMouseListener(this); + + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Seperator + + 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); + viewport.applet.validate(); + + } + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; + MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + Menu formatMenu = new Menu(); + Menu selectMenu = new Menu(); + MenuItem newView = new MenuItem(); + + public void mousePressed(MouseEvent evt) + { + PopupMenu popup = null; + Label source = (Label) evt.getSource(); + if (source == embeddedFile) + { + popup = filePopup = genPopupMenu(filePopup, fileMenu); + } + else if (source == embeddedEdit) + { + popup = editPopup = genPopupMenu(editPopup, editMenu); + } + else if (source == embeddedSelect) + { + popup = searchPopup = genPopupMenu(searchPopup, selectMenu); + } + else if (source == embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); + } + else if (source == embeddedFormat) + { + popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + } + else if (source == embeddedColour) + { + popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + } + else if (source == embeddedCalculate) + { + popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + } + else if (source == embeddedHelp) + { + popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + } + + embeddedMenu.add(popup); + popup.show(embeddedMenu, + source.getBounds().x, + source.getBounds().y + source.getBounds().getSize().height); + } + + PopupMenu genPopupMenu(PopupMenu popup, Menu original) + { + if (popup != null) + { + return popup; + } + popup = new PopupMenu(); + int m, mSize = original.getItemCount(); + for (m = 0; m < mSize; m++) + { + popup.add(original.getItem(m)); + mSize--; + m--; + } + + return popup; + } + + public void mouseClicked(MouseEvent evt) + {} + + public void mouseReleased(MouseEvent evt) + {} + + public void mouseEntered(MouseEvent evt) + {} + + public void mouseExited(MouseEvent evt) + {} + +} diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 23180ce..9881b64 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,322 +1,322 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.commands.*; -import jalview.datamodel.*; - -public class RedundancyPanel - extends SliderPanel implements Runnable, WindowListener -{ - AlignmentPanel ap; - - Stack historyList = new Stack(); // simpler than synching with alignFrame. - float[] redundancy; - SequenceI[] originalSequences; - Frame frame; - Vector redundantSeqs; - - public RedundancyPanel(AlignmentPanel ap) - { - super(ap, 0, false, null); - - redundantSeqs = new Vector(); - this.ap = ap; - undoButton.setVisible(true); - applyButton.setVisible(true); - allGroupsCheck.setVisible(false); - - label.setText("Enter the redundancy threshold"); - valueField.setText("100"); - - slider.setVisibleAmount(1); - slider.setMinimum(0); - slider.setMaximum(100 + slider.getVisibleAmount()); - slider.setValue(100); - - slider.addAdjustmentListener(new AdjustmentListener() - { - public void adjustmentValueChanged(AdjustmentEvent evt) - { - valueField.setText(slider.getValue() + ""); - sliderValueChanged(); - } - }); - - frame = new Frame(); - frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 100); - - frame.addWindowListener(this); - - Thread worker = new Thread(this); - worker.start(); - } - - /** - * This is a copy of remove redundancy in jalivew.datamodel.Alignment - * except we dont want to remove redundancy, just calculate once - * so we can use the slider to dynamically hide redundant sequences - * - * @param threshold DOCUMENT ME! - * @param sel DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public void run() - { - label.setText("Calculating...."); - - slider.setVisible(false); - applyButton.setEnabled(false); - valueField.setVisible(false); - - validate(); - - String[] omitHidden = null; - - SequenceGroup sg = ap.av.getSelectionGroup(); - int height; - - int start, end; - - if ( (sg != null) && (sg.getSize() >= 1)) - { - originalSequences = sg.getSequencesInOrder(ap.av.alignment); - start = sg.getStartRes(); - end = sg.getEndRes(); - } - else - { - originalSequences = ap.av.alignment.getSequencesArray(); - start = 0; - end = ap.av.alignment.getWidth(); - } - - height = originalSequences.length; - - redundancy = new float[height]; - for (int i = 0; i < height; i++) - { - redundancy[i] = 0f; - } - - // if (ap.av.hasHiddenColumns) - { - // omitHidden = ap.av.getSelectionAsString(); - } - - // long start = System.currentTimeMillis(); - - float pid; - String seqi, seqj; - for (int i = 0; i < height; i++) - { - for (int j = 0; j < i; j++) - { - if (i == j) - { - continue; - } - - if (omitHidden == null) - { - seqi = originalSequences[i].getSequenceAsString(start, end); - seqj = originalSequences[j].getSequenceAsString(start, end); - } - else - { - seqi = omitHidden[i]; - seqj = omitHidden[j]; - } - - pid = jalview.util.Comparison.PID(seqi, seqj); - - if (seqj.length() < seqi.length()) - { - redundancy[j] = Math.max(pid, redundancy[j]); - } - else - { - redundancy[i] = Math.max(pid, redundancy[i]); - } - - } - } - - label.setText("Enter the redundancy threshold"); - slider.setVisible(true); - applyButton.setEnabled(true); - valueField.setVisible(true); - - validate(); - // System.out.println("blob done "+ (System.currentTimeMillis()-start)); - } - - void sliderValueChanged() - { - if (redundancy == null) - { - return; - } - - float value = slider.getValue(); - - for (int i = 0; i < redundancy.length; i++) - { - if (value > redundancy[i]) - { - redundantSeqs.removeElement(originalSequences[i]); - } - else if (!redundantSeqs.contains(originalSequences[i])) - { - redundantSeqs.addElement(originalSequences[i]); - } - } - - ap.idPanel.idCanvas.setHighlighted(redundantSeqs); - PaintRefresher.Refresh(this, - ap.av.getSequenceSetId(), - true, - true); - - } - - public void applyButton_actionPerformed() - { - Vector del = new Vector(); - - undoButton.setEnabled(true); - - float value = slider.getValue(); - SequenceGroup sg = ap.av.getSelectionGroup(); - - for (int i = 0; i < redundancy.length; i++) - { - if (value <= redundancy[i]) - { - del.addElement(originalSequences[i]); - } - } - - // This has to be done before the restoreHistoryItem method of alignFrame will - // actually restore these sequences. - if (del.size() > 0) - { - SequenceI[] deleted = new SequenceI[del.size()]; - - int width = 0; - for (int i = 0; i < del.size(); i++) - { - deleted[i] = (SequenceI) del.elementAt(i); - if (deleted[i].getLength() > width) - { - width = deleted[i].getLength(); - } - } - - EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, - ap.av.alignment); - - for (int i = 0; i < del.size(); i++) - { - ap.av.alignment.deleteSequence(deleted[i]); - PaintRefresher.Refresh(this, - ap.av.getSequenceSetId(), - true, - true); - if (sg != null) - { - sg.deleteSequence(deleted[i], false); - } - } - - historyList.push(cut); - - ap.alignFrame.addHistoryItem(cut); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } - - } - - public void undoButton_actionPerformed() - { - CommandI command = (CommandI) historyList.pop(); - command.undoCommand(); - - if (ap.av.historyList.contains(command)) - { - ap.av.historyList.removeElement(command); - ap.alignFrame.updateEditMenuBar(); - } - - ap.paintAlignment(true); - - if (historyList.size() == 0) - { - undoButton.setEnabled(false); - } - } - - public void valueField_actionPerformed(ActionEvent e) - { - try - { - int i = Integer.parseInt(valueField.getText()); - slider.setValue(i); - } - catch (Exception ex) - { - valueField.setText(slider.getValue() + ""); - } - } - - public void windowOpened(WindowEvent evt) - {} - - public void windowClosing(WindowEvent evt) - { - ap.idPanel.idCanvas.setHighlighted(null); - } - - public void windowClosed(WindowEvent evt) - {} - - public void windowActivated(WindowEvent evt) - {} - - public void windowDeactivated(WindowEvent evt) - {} - - public void windowIconified(WindowEvent evt) - {} - - public void windowDeiconified(WindowEvent evt) - {} -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +package jalview.appletgui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.commands.*; +import jalview.datamodel.*; + +public class RedundancyPanel + extends SliderPanel implements Runnable, WindowListener +{ + AlignmentPanel ap; + + Stack historyList = new Stack(); // simpler than synching with alignFrame. + float[] redundancy; + SequenceI[] originalSequences; + Frame frame; + Vector redundantSeqs; + + public RedundancyPanel(AlignmentPanel ap) + { + super(ap, 0, false, null); + + redundantSeqs = new Vector(); + this.ap = ap; + undoButton.setVisible(true); + applyButton.setVisible(true); + allGroupsCheck.setVisible(false); + + label.setText("Enter the redundancy threshold"); + valueField.setText("100"); + + slider.setVisibleAmount(1); + slider.setMinimum(0); + slider.setMaximum(100 + slider.getVisibleAmount()); + slider.setValue(100); + + slider.addAdjustmentListener(new AdjustmentListener() + { + public void adjustmentValueChanged(AdjustmentEvent evt) + { + valueField.setText(slider.getValue() + ""); + sliderValueChanged(); + } + }); + + frame = new Frame(); + frame.add(this); + jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", + 400, 100); + + frame.addWindowListener(this); + + Thread worker = new Thread(this); + worker.start(); + } + + /** + * This is a copy of remove redundancy in jalivew.datamodel.Alignment + * except we dont want to remove redundancy, just calculate once + * so we can use the slider to dynamically hide redundant sequences + * + * @param threshold DOCUMENT ME! + * @param sel DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public void run() + { + label.setText("Calculating...."); + + slider.setVisible(false); + applyButton.setEnabled(false); + valueField.setVisible(false); + + validate(); + + String[] omitHidden = null; + + SequenceGroup sg = ap.av.getSelectionGroup(); + int height; + + int start, end; + + if ( (sg != null) && (sg.getSize() >= 1)) + { + originalSequences = sg.getSequencesInOrder(ap.av.alignment); + start = sg.getStartRes(); + end = sg.getEndRes(); + } + else + { + originalSequences = ap.av.alignment.getSequencesArray(); + start = 0; + end = ap.av.alignment.getWidth(); + } + + height = originalSequences.length; + + redundancy = new float[height]; + for (int i = 0; i < height; i++) + { + redundancy[i] = 0f; + } + + // if (ap.av.hasHiddenColumns) + { + // omitHidden = ap.av.getSelectionAsString(); + } + + // long start = System.currentTimeMillis(); + + float pid; + String seqi, seqj; + for (int i = 0; i < height; i++) + { + for (int j = 0; j < i; j++) + { + if (i == j) + { + continue; + } + + if (omitHidden == null) + { + seqi = originalSequences[i].getSequenceAsString(start, end); + seqj = originalSequences[j].getSequenceAsString(start, end); + } + else + { + seqi = omitHidden[i]; + seqj = omitHidden[j]; + } + + pid = jalview.util.Comparison.PID(seqi, seqj); + + if (seqj.length() < seqi.length()) + { + redundancy[j] = Math.max(pid, redundancy[j]); + } + else + { + redundancy[i] = Math.max(pid, redundancy[i]); + } + + } + } + + label.setText("Enter the redundancy threshold"); + slider.setVisible(true); + applyButton.setEnabled(true); + valueField.setVisible(true); + + validate(); + // System.out.println("blob done "+ (System.currentTimeMillis()-start)); + } + + void sliderValueChanged() + { + if (redundancy == null) + { + return; + } + + float value = slider.getValue(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value > redundancy[i]) + { + redundantSeqs.removeElement(originalSequences[i]); + } + else if (!redundantSeqs.contains(originalSequences[i])) + { + redundantSeqs.addElement(originalSequences[i]); + } + } + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); + PaintRefresher.Refresh(this, + ap.av.getSequenceSetId(), + true, + true); + + } + + public void applyButton_actionPerformed() + { + Vector del = new Vector(); + + undoButton.setEnabled(true); + + float value = slider.getValue(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value <= redundancy[i]) + { + del.addElement(originalSequences[i]); + } + } + + // This has to be done before the restoreHistoryItem method of alignFrame will + // actually restore these sequences. + if (del.size() > 0) + { + SequenceI[] deleted = new SequenceI[del.size()]; + + int width = 0; + for (int i = 0; i < del.size(); i++) + { + deleted[i] = (SequenceI) del.elementAt(i); + if (deleted[i].getLength() > width) + { + width = deleted[i].getLength(); + } + } + + EditCommand cut = new EditCommand("Remove Redundancy", + EditCommand.CUT, deleted, 0, width, + ap.av.alignment); + + for (int i = 0; i < del.size(); i++) + { + ap.av.alignment.deleteSequence(deleted[i]); + PaintRefresher.Refresh(this, + ap.av.getSequenceSetId(), + true, + true); + if (sg != null) + { + sg.deleteSequence(deleted[i], false); + } + } + + historyList.push(cut); + + ap.alignFrame.addHistoryItem(cut); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + + } + + public void undoButton_actionPerformed() + { + CommandI command = (CommandI) historyList.pop(); + command.undoCommand(null); + + if (ap.av.historyList.contains(command)) + { + ap.av.historyList.removeElement(command); + ap.alignFrame.updateEditMenuBar(); + } + + ap.paintAlignment(true); + + if (historyList.size() == 0) + { + undoButton.setEnabled(false); + } + } + + public void valueField_actionPerformed(ActionEvent e) + { + try + { + int i = Integer.parseInt(valueField.getText()); + slider.setValue(i); + } + catch (Exception ex) + { + valueField.setText(slider.getValue() + ""); + } + } + + public void windowOpened(WindowEvent evt) + {} + + public void windowClosing(WindowEvent evt) + { + ap.idPanel.idCanvas.setHighlighted(null); + } + + public void windowClosed(WindowEvent evt) + {} + + public void windowActivated(WindowEvent evt) + {} + + public void windowDeactivated(WindowEvent evt) + {} + + public void windowIconified(WindowEvent evt) + {} + + public void windowDeiconified(WindowEvent evt) + {} +} diff --git a/src/jalview/commands/ChangeCaseCommand.java b/src/jalview/commands/ChangeCaseCommand.java index d34552d..976be92 100644 --- a/src/jalview/commands/ChangeCaseCommand.java +++ b/src/jalview/commands/ChangeCaseCommand.java @@ -1,133 +1,133 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.commands; - -import jalview.datamodel.*; - -public class ChangeCaseCommand - implements CommandI -{ - String description; - public static int TO_LOWER = 0; - public static int TO_UPPER = 1; - public static int TOGGLE_CASE = 2; - int caseChange = -1; - SequenceI[] seqs; - int[][] regions; - public ChangeCaseCommand(String description, - SequenceI[] seqs, - int[][] regions, - int caseChange) - { - this.description = description; - this.seqs = seqs; - this.regions = regions; - this.caseChange = caseChange; - doCommand(); - } - - public String getDescription() - { - return description; - } - - public int getSize() - { - return 1; - } - - public void doCommand() - { - changeCase(true); - } - - public void undoCommand() - { - changeCase(false); - } - - void changeCase(boolean doCommand) - { - String sequence; - int start, end; - char nextChar; - for (int r = 0; r < regions.length; r++) - { - start = regions[r][0]; - for (int s = 0; s < seqs.length; s++) - { - sequence = seqs[s].getSequenceAsString(); - StringBuffer newSeq = new StringBuffer(); - - if (regions[r][1] > sequence.length()) - { - end = sequence.length(); - } - else - { - end = regions[r][1]; - } - - if (start > 0) - { - newSeq.append(sequence.substring(0, start)); - } - - if ( (caseChange == TO_UPPER && doCommand) - || (caseChange == TO_LOWER && !doCommand)) - { - newSeq.append(sequence.substring(start, end).toUpperCase()); - } - - else if ( (caseChange == TO_LOWER && doCommand) - || (caseChange == TO_UPPER && !doCommand)) - { - newSeq.append(sequence.substring(start, end).toLowerCase()); - } - - else //TOGGLE CASE - { - for (int c = start; c < end; c++) - { - nextChar = sequence.charAt(c); - if ('a' <= nextChar && nextChar <= 'z') - { - // TO UPPERCASE !!! - nextChar -= ('a' - 'A'); - } - else if ('A' <= nextChar && nextChar <= 'Z') - { - // TO LOWERCASE !!! - nextChar += ('a' - 'A'); - } - newSeq.append(nextChar); - } - } - - if (end < sequence.length()) - { - newSeq.append(sequence.substring(end)); - } - - seqs[s].setSequence(newSeq.toString()); - } - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.commands; + +import jalview.datamodel.*; + +public class ChangeCaseCommand + implements CommandI +{ + String description; + public static int TO_LOWER = 0; + public static int TO_UPPER = 1; + public static int TOGGLE_CASE = 2; + int caseChange = -1; + SequenceI[] seqs; + int[][] regions; + public ChangeCaseCommand(String description, + SequenceI[] seqs, + int[][] regions, + int caseChange) + { + this.description = description; + this.seqs = seqs; + this.regions = regions; + this.caseChange = caseChange; + doCommand(null); + } + + public String getDescription() + { + return description; + } + + public int getSize() + { + return 1; + } + + public void doCommand(AlignmentI[] views) + { + changeCase(true); + } + + public void undoCommand(AlignmentI[] views) + { + changeCase(false); + } + + void changeCase(boolean doCommand) + { + String sequence; + int start, end; + char nextChar; + for (int r = 0; r < regions.length; r++) + { + start = regions[r][0]; + for (int s = 0; s < seqs.length; s++) + { + sequence = seqs[s].getSequenceAsString(); + StringBuffer newSeq = new StringBuffer(); + + if (regions[r][1] > sequence.length()) + { + end = sequence.length(); + } + else + { + end = regions[r][1]; + } + + if (start > 0) + { + newSeq.append(sequence.substring(0, start)); + } + + if ( (caseChange == TO_UPPER && doCommand) + || (caseChange == TO_LOWER && !doCommand)) + { + newSeq.append(sequence.substring(start, end).toUpperCase()); + } + + else if ( (caseChange == TO_LOWER && doCommand) + || (caseChange == TO_UPPER && !doCommand)) + { + newSeq.append(sequence.substring(start, end).toLowerCase()); + } + + else //TOGGLE CASE + { + for (int c = start; c < end; c++) + { + nextChar = sequence.charAt(c); + if ('a' <= nextChar && nextChar <= 'z') + { + // TO UPPERCASE !!! + nextChar -= ('a' - 'A'); + } + else if ('A' <= nextChar && nextChar <= 'Z') + { + // TO LOWERCASE !!! + nextChar += ('a' - 'A'); + } + newSeq.append(nextChar); + } + } + + if (end < sequence.length()) + { + newSeq.append(sequence.substring(end)); + } + + seqs[s].setSequence(newSeq.toString()); + } + } + } + +} diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java index d97a6bb..97675e7 100644 --- a/src/jalview/commands/CommandI.java +++ b/src/jalview/commands/CommandI.java @@ -1,30 +1,30 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.commands; - -public interface CommandI -{ - public void doCommand(); - - public void undoCommand(); - - public String getDescription(); - - public int getSize(); -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.commands; + +public interface CommandI +{ + public void doCommand(jalview.datamodel.AlignmentI[] views); + + public void undoCommand(jalview.datamodel.AlignmentI[] views); + + public String getDescription(); + + public int getSize(); +} diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index cbcc700..aece057 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -73,7 +73,7 @@ public class EditCommand new Edit(command, seqs, position, number, al)}; } - performEdit(0); + performEdit(0, null); } public EditCommand(String description, @@ -91,7 +91,7 @@ public class EditCommand { new Edit(command, seqs, position, number, al, replace)}; } - performEdit(0); + performEdit(0, null); } final public String getDescription() @@ -109,12 +109,42 @@ public class EditCommand return edits[0].al; } + /** + * append a new editCommand + * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced + * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter. + * @param command + * @param seqs + * @param position + * @param number + * @param al + * @param performEdit + */ + final public void appendEdit(int command, + SequenceI[] seqs, + int position, + int number, + AlignmentI al, + boolean performEdit) + { + appendEdit(command, seqs, position, number, al, performEdit, null); + } + /** + * append a new edit command with a set of alignment views that may be operated on + * @param command + * @param seqs + * @param position + * @param number + * @param al + * @param performEdit + * @param views + */ final public void appendEdit(int command, SequenceI[] seqs, int position, int number, AlignmentI al, - boolean performEdit) + boolean performEdit, AlignmentI[] views) { Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter()); if (al.getHeight() == seqs.length) @@ -139,11 +169,11 @@ public class EditCommand if (performEdit) { - performEdit(edits.length - 1); + performEdit(edits.length - 1, views); } } - final void performEdit(int commandIndex) + final void performEdit(int commandIndex, AlignmentI[] views) { int eSize = edits.length; for (int e = commandIndex; e < eSize; e++) @@ -157,10 +187,10 @@ public class EditCommand deleteGap(edits[e]); break; case CUT: - cut(edits[e]); + cut(edits[e], views); break; case PASTE: - paste(edits[e]); + paste(edits[e], views); break; case REPLACE: replace(edits[e]); @@ -169,12 +199,12 @@ public class EditCommand } } - final public void doCommand() + final public void doCommand(AlignmentI[] views) { - performEdit(0); + performEdit(0,views); } - final public void undoCommand() + final public void undoCommand(AlignmentI[] views) { int e = 0, eSize = edits.length; for (e = eSize - 1; e > -1; e--) @@ -188,10 +218,10 @@ public class EditCommand insertGap(edits[e]); break; case CUT: - paste(edits[e]); + paste(edits[e], views); break; case PASTE: - cut(edits[e]); + cut(edits[e], views); break; case REPLACE: replace(edits[e]); @@ -209,7 +239,7 @@ public class EditCommand command.gapChar); } - adjustAnnotations(command, true, false); + adjustAnnotations(command, true, false, null); } final void deleteGap(Edit command) @@ -220,10 +250,10 @@ public class EditCommand command.position + command.number); } - adjustAnnotations(command, false, false); + adjustAnnotations(command, false, false, null); } - void cut(Edit command) + void cut(Edit command, AlignmentI[] views) { boolean seqDeleted=false; command.string = new char[command.seqs.length][]; @@ -264,10 +294,10 @@ public class EditCommand } } - adjustAnnotations(command, false, seqDeleted); + adjustAnnotations(command, false, seqDeleted, views); } - void paste(Edit command) + void paste(Edit command, AlignmentI[] views) { StringBuffer tmp; boolean newDSNeeded; @@ -345,7 +375,7 @@ public class EditCommand adjustFeatures(command, i, start, end, true); } } - adjustAnnotations(command, true, seqWasDeleted); + adjustAnnotations(command, true, seqWasDeleted, views); command.string = null; } @@ -371,7 +401,7 @@ public class EditCommand } } - final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility) + final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views) { AlignmentAnnotation[] annotations = null; @@ -398,12 +428,55 @@ public class EditCommand // remove rows tmp = command.seqs[s].getAnnotation(); if (tmp!=null) { - command.deletedAnnotationRows.put(command.seqs[s], tmp); + int alen=tmp.length; for (int aa =0; aa i) - { - if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i))) - { - if (delete) - { - endCol = i; - } - - delete = false; - break; - } - } - } - - if (delete && startCol == -1) - { - startCol = i; - } - - if (!delete && startCol > -1) - { - this.appendEdit(DELETE_GAP, seqs, - startCol - columnsDeleted, - endCol - startCol, - al, - false); - - columnsDeleted += (endCol - startCol); - startCol = -1; - endCol = -1; - } - } - - if (delete && startCol > -1) - { - //This is for empty columns at the - //end of the alignment - - this.appendEdit(DELETE_GAP, seqs, - startCol - columnsDeleted, - end - startCol + 1, - al, - false); - - columnsDeleted += (end - startCol + 1); - } - - performEdit(0); - } - - public int getSize() - { - //We're interested in the number of columns deleted, - //Not the number of sequence edits. - return columnsDeleted; - } - -} +package jalview.commands; + +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +import jalview.datamodel.*; + +public class RemoveGapColCommand + extends EditCommand +{ + int columnsDeleted; + public RemoveGapColCommand(String description, + SequenceI[] seqs, + int start, int end, AlignmentI al) + { + this.description = description; + + int j, jSize = seqs.length; + + int startCol = -1, endCol = -1; + columnsDeleted = 0; + + edits = new Edit[0]; + + boolean delete = true; + for (int i = start; i <= end; i++) + { + delete = true; + + for (j = 0; j < jSize; j++) + { + if (seqs[j].getLength() > i) + { + if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i))) + { + if (delete) + { + endCol = i; + } + + delete = false; + break; + } + } + } + + if (delete && startCol == -1) + { + startCol = i; + } + + if (!delete && startCol > -1) + { + this.appendEdit(DELETE_GAP, seqs, + startCol - columnsDeleted, + endCol - startCol, + al, + false,null); + + columnsDeleted += (endCol - startCol); + startCol = -1; + endCol = -1; + } + } + + if (delete && startCol > -1) + { + //This is for empty columns at the + //end of the alignment + + this.appendEdit(DELETE_GAP, seqs, + startCol - columnsDeleted, + end - startCol + 1, + al, + false,null); + + columnsDeleted += (end - startCol + 1); + } + + performEdit(0,null); + } + + public int getSize() + { + //We're interested in the number of columns deleted, + //Not the number of sequence edits. + return columnsDeleted; + } + +} diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java index ccc8008..5639fa5 100644 --- a/src/jalview/commands/RemoveGapsCommand.java +++ b/src/jalview/commands/RemoveGapsCommand.java @@ -1,120 +1,120 @@ -package jalview.commands; - -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -import jalview.datamodel.*; - -public class RemoveGapsCommand - extends EditCommand -{ - public RemoveGapsCommand(String description, - SequenceI[] seqs, AlignmentI al) - { - this.description = description; - int width = 0; - for (int i = 0; i < seqs.length; i++) - { - if (seqs[i].getLength() > width) - { - width = seqs[i].getLength(); - } - } - - findGaps(seqs, 0, width, al); - } - - public RemoveGapsCommand(String description, - SequenceI[] seqs, - int start, int end, AlignmentI al) - { - this.description = description; - findGaps(seqs, start, end, al); - } - - void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al) - { - - int startCol = -1, endCol = -1; - int deletedCols = 0; - - int j, jSize; - - edits = new Edit[0]; - - boolean delete = true; - char[] sequence; - - for (int s = 0; s < seqs.length; s++) - { - deletedCols = 0; - startCol = -1; - endCol = -1; - sequence = seqs[s].getSequence(start, end + 1); - - jSize = sequence.length; - for (j = 0; j < jSize; j++) - { - delete = true; - - if (!jalview.util.Comparison.isGap(sequence[j])) - { - if (delete) - { - endCol = j; - } - - delete = false; - } - - if (delete && startCol == -1) - { - startCol = j; - } - - if (!delete && startCol > -1) - { - this.appendEdit(DELETE_GAP, new SequenceI[] - {seqs[s]}, - start + startCol - deletedCols, - endCol - startCol, - al, - false); - - deletedCols += (endCol - startCol); - startCol = -1; - endCol = -1; - } - } - if (delete && startCol > -1) - { - this.appendEdit(DELETE_GAP, new SequenceI[] - {seqs[s]}, - start + startCol - deletedCols, - jSize - startCol, - al, - false); - } - - } - - performEdit(0); - } - -} +package jalview.commands; + +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +import jalview.datamodel.*; + +public class RemoveGapsCommand + extends EditCommand +{ + public RemoveGapsCommand(String description, + SequenceI[] seqs, AlignmentI al) + { + this.description = description; + int width = 0; + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i].getLength() > width) + { + width = seqs[i].getLength(); + } + } + + findGaps(seqs, 0, width, al); + } + + public RemoveGapsCommand(String description, + SequenceI[] seqs, + int start, int end, AlignmentI al) + { + this.description = description; + findGaps(seqs, start, end, al); + } + + void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al) + { + + int startCol = -1, endCol = -1; + int deletedCols = 0; + + int j, jSize; + + edits = new Edit[0]; + + boolean delete = true; + char[] sequence; + + for (int s = 0; s < seqs.length; s++) + { + deletedCols = 0; + startCol = -1; + endCol = -1; + sequence = seqs[s].getSequence(start, end + 1); + + jSize = sequence.length; + for (j = 0; j < jSize; j++) + { + delete = true; + + if (!jalview.util.Comparison.isGap(sequence[j])) + { + if (delete) + { + endCol = j; + } + + delete = false; + } + + if (delete && startCol == -1) + { + startCol = j; + } + + if (!delete && startCol > -1) + { + this.appendEdit(DELETE_GAP, new SequenceI[] + {seqs[s]}, + start + startCol - deletedCols, + endCol - startCol, + al, + false,null); + + deletedCols += (endCol - startCol); + startCol = -1; + endCol = -1; + } + } + if (delete && startCol > -1) + { + this.appendEdit(DELETE_GAP, new SequenceI[] + {seqs[s]}, + start + startCol - deletedCols, + jSize - startCol, + al, + false,null); + } + + } + + performEdit(0,null); + } + +} diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java index 21385ad..9b9c99e 100644 --- a/src/jalview/commands/SlideSequencesCommand.java +++ b/src/jalview/commands/SlideSequencesCommand.java @@ -1,93 +1,93 @@ - -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ - -package jalview.commands; - -import jalview.datamodel.*; - -public class SlideSequencesCommand extends EditCommand -{ - boolean gapsInsertedBegin = false; - - public SlideSequencesCommand(String description, - SequenceI[] seqsLeft, - SequenceI[] seqsRight, - int slideSize, - char gapChar) - { - this.description = description; - - int lSize = seqsLeft.length; - gapsInsertedBegin = false; - int i, j; - for (i = 0; i < lSize; i++) - { - for (j = 0; j < slideSize; j++) - if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j))) - { - gapsInsertedBegin = true; - break; - } - } - - if (!gapsInsertedBegin) - edits = new Edit[] - { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)}; - else - edits = new Edit[] - { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)}; - - performEdit(0); - } - - public boolean getGapsInsertedBegin() - { - return gapsInsertedBegin; - } - - public boolean appendSlideCommand(SlideSequencesCommand command) - { - boolean same = false; - - if(command.edits[0].seqs.length==edits[0].seqs.length) - { - same = true; - for (int i = 0; i < command.edits[0].seqs.length; i++) - { - if (edits[0].seqs[i] != command.edits[0].seqs[i]) - { - same = false; - } - } - } - - if(same) - { - Edit[] temp = new Edit[command.edits.length + 1]; - System.arraycopy(command.edits, 0, temp, 0, command.edits.length); - command.edits = temp; - command.edits[command.edits.length - 1] = edits[0]; - } - - return same; - } -} - - + +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program is free software; you can redistribute it and/or +* modify it under the terms of the GNU General Public License +* as published by the Free Software Foundation; either version 2 +* of the License, or (at your option) any later version. +* +* This program is distributed in the hope that it will be useful, +* but WITHOUT ANY WARRANTY; without even the implied warranty of +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +* GNU General Public License for more details. +* +* You should have received a copy of the GNU General Public License +* along with this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ + +package jalview.commands; + +import jalview.datamodel.*; + +public class SlideSequencesCommand extends EditCommand +{ + boolean gapsInsertedBegin = false; + + public SlideSequencesCommand(String description, + SequenceI[] seqsLeft, + SequenceI[] seqsRight, + int slideSize, + char gapChar) + { + this.description = description; + + int lSize = seqsLeft.length; + gapsInsertedBegin = false; + int i, j; + for (i = 0; i < lSize; i++) + { + for (j = 0; j < slideSize; j++) + if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j))) + { + gapsInsertedBegin = true; + break; + } + } + + if (!gapsInsertedBegin) + edits = new Edit[] + { new Edit(DELETE_GAP, seqsLeft, 0, slideSize, gapChar)}; + else + edits = new Edit[] + { new Edit(INSERT_GAP, seqsRight, 0, slideSize, gapChar)}; + + performEdit(0,null); + } + + public boolean getGapsInsertedBegin() + { + return gapsInsertedBegin; + } + + public boolean appendSlideCommand(SlideSequencesCommand command) + { + boolean same = false; + + if(command.edits[0].seqs.length==edits[0].seqs.length) + { + same = true; + for (int i = 0; i < command.edits[0].seqs.length; i++) + { + if (edits[0].seqs[i] != command.edits[0].seqs[i]) + { + same = false; + } + } + } + + if(same) + { + Edit[] temp = new Edit[command.edits.length + 1]; + System.arraycopy(command.edits, 0, temp, 0, command.edits.length); + command.edits = temp; + command.edits[command.edits.length - 1] = edits[0]; + } + + return same; + } +} + + diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java index 4c1dea0..4110bd1 100644 --- a/src/jalview/commands/TrimRegionCommand.java +++ b/src/jalview/commands/TrimRegionCommand.java @@ -1,178 +1,178 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.commands; - -import java.util.*; - -import jalview.datamodel.*; -import jalview.util.*; - -public class TrimRegionCommand - extends EditCommand -{ - public static String TRIM_LEFT = "TrimLeft"; - public static String TRIM_RIGHT = "TrimRight"; - - public ColumnSelection colSel = null; - - int[] start; - - ShiftList shiftList; - - SequenceGroup selectionGroup; - - Vector deletedHiddenColumns; - - int columnsDeleted; - - public TrimRegionCommand(String description, - String command, - SequenceI[] seqs, - int column, - AlignmentI al, - ColumnSelection colSel, - SequenceGroup selectedRegion) - { - this.description = description; - this.selectionGroup = selectedRegion; - this.colSel = colSel; - if (command.equalsIgnoreCase(TRIM_LEFT)) - { - if (column == 0) - { - return; - } - - columnsDeleted = column; - - edits = new Edit[] - { - new Edit(CUT, seqs, 0, column, al)}; - } - else if (command.equalsIgnoreCase(TRIM_RIGHT)) - { - int width = al.getWidth() - column - 1; - if (width < 2) - { - return; - } - - columnsDeleted = width - 1; - - edits = new Edit[] - { - new Edit(CUT, seqs, column + 1, width, al)}; - } - - //We need to keep a record of the sequence start - //in order to restore the state after a redo - int i, isize = edits[0].seqs.length; - start = new int[isize]; - for (i = 0; i < isize; i++) - { - start[i] = edits[0].seqs[i].getStart(); - } - - performEdit(0); - } - - void cut(Edit command) - { - int column, j, jSize = command.seqs.length; - for (j = 0; j < jSize; j++) - { - if (command.position == 0) - { - //This is a TRIM_LEFT command - column = command.seqs[j].findPosition(command.number); - command.seqs[j].setStart(column); - } - else - { - //This is a TRIM_RIGHT command - column = command.seqs[j].findPosition(command.position) - 1; - command.seqs[j].setEnd(column); - } - } - - super.cut(command); - - if (command.position == 0) - { - deletedHiddenColumns = colSel.compensateForEdit(0, command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveLeft(command.number); - } - } - else - { - deletedHiddenColumns = colSel.compensateForEdit(command.position, - command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveRight(command.position); - } - } - } - - void paste(Edit command) - { - super.paste(command); - int column, j, jSize = command.seqs.length; - for (j = 0; j < jSize; j++) - { - if (command.position == 0) - { - command.seqs[j].setStart(start[j]); - } - else - { - column = command.seqs[j] - .findPosition(command.number + command.position) - 1; - command.seqs[j].setEnd(column); - } - } - - if (command.position == 0) - { - colSel.compensateForEdit(0, -command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveLeft( -command.number); - } - } - - if (deletedHiddenColumns != null) - { - int[] region; - for (int i = 0; i < deletedHiddenColumns.size(); i++) - { - region = (int[]) deletedHiddenColumns.elementAt(i); - colSel.hideColumns(region[0], region[1]); - } - } - } - - public int getSize() - { - return columnsDeleted; - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.commands; + +import java.util.*; + +import jalview.datamodel.*; +import jalview.util.*; + +public class TrimRegionCommand + extends EditCommand +{ + public static String TRIM_LEFT = "TrimLeft"; + public static String TRIM_RIGHT = "TrimRight"; + + public ColumnSelection colSel = null; + + int[] start; + + ShiftList shiftList; + + SequenceGroup selectionGroup; + + Vector deletedHiddenColumns; + + int columnsDeleted; + + public TrimRegionCommand(String description, + String command, + SequenceI[] seqs, + int column, + AlignmentI al, + ColumnSelection colSel, + SequenceGroup selectedRegion) + { + this.description = description; + this.selectionGroup = selectedRegion; + this.colSel = colSel; + if (command.equalsIgnoreCase(TRIM_LEFT)) + { + if (column == 0) + { + return; + } + + columnsDeleted = column; + + edits = new Edit[] + { + new Edit(CUT, seqs, 0, column, al)}; + } + else if (command.equalsIgnoreCase(TRIM_RIGHT)) + { + int width = al.getWidth() - column - 1; + if (width < 2) + { + return; + } + + columnsDeleted = width - 1; + + edits = new Edit[] + { + new Edit(CUT, seqs, column + 1, width, al)}; + } + + //We need to keep a record of the sequence start + //in order to restore the state after a redo + int i, isize = edits[0].seqs.length; + start = new int[isize]; + for (i = 0; i < isize; i++) + { + start[i] = edits[0].seqs[i].getStart(); + } + + performEdit(0,null); + } + + void cut(Edit command) + { + int column, j, jSize = command.seqs.length; + for (j = 0; j < jSize; j++) + { + if (command.position == 0) + { + //This is a TRIM_LEFT command + column = command.seqs[j].findPosition(command.number); + command.seqs[j].setStart(column); + } + else + { + //This is a TRIM_RIGHT command + column = command.seqs[j].findPosition(command.position) - 1; + command.seqs[j].setEnd(column); + } + } + + super.cut(command, null); + + if (command.position == 0) + { + deletedHiddenColumns = colSel.compensateForEdit(0, command.number); + if (selectionGroup != null) + { + selectionGroup.adjustForRemoveLeft(command.number); + } + } + else + { + deletedHiddenColumns = colSel.compensateForEdit(command.position, + command.number); + if (selectionGroup != null) + { + selectionGroup.adjustForRemoveRight(command.position); + } + } + } + + void paste(Edit command) + { + super.paste(command, null); + int column, j, jSize = command.seqs.length; + for (j = 0; j < jSize; j++) + { + if (command.position == 0) + { + command.seqs[j].setStart(start[j]); + } + else + { + column = command.seqs[j] + .findPosition(command.number + command.position) - 1; + command.seqs[j].setEnd(column); + } + } + + if (command.position == 0) + { + colSel.compensateForEdit(0, -command.number); + if (selectionGroup != null) + { + selectionGroup.adjustForRemoveLeft( -command.number); + } + } + + if (deletedHiddenColumns != null) + { + int[] region; + for (int i = 0; i < deletedHiddenColumns.size(); i++) + { + region = (int[]) deletedHiddenColumns.elementAt(i); + colSel.hideColumns(region[0], region[1]); + } + } + } + + public int getSize() + { + return columnsDeleted; + } + +} diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 6f5b09d..1e51879 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,335 +1,335 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import java.util.*; - -import java.awt.event.*; -import javax.swing.*; -import javax.swing.event.*; - -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.util.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class RedundancyPanel - extends GSliderPanel implements Runnable -{ - AlignFrame af; - AlignmentPanel ap; - Stack historyList = new Stack(); // simpler than synching with alignFrame. - float[] redundancy; - SequenceI[] originalSequences; - JInternalFrame frame; - Vector redundantSeqs; - - /** - * Creates a new RedundancyPanel object. - * - * @param ap DOCUMENT ME! - * @param af DOCUMENT ME! - */ - public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) - { - this.ap = ap; - this.af = af; - redundantSeqs = new Vector(); - - slider.addChangeListener(new ChangeListener() - { - public void stateChanged(ChangeEvent evt) - { - valueField.setText(slider.getValue() + ""); - sliderValueChanged(); - } - }); - - applyButton.setText("Remove"); - allGroupsCheck.setVisible(false); - slider.setMinimum(0); - slider.setMaximum(100); - slider.setValue(100); - - Thread worker = new Thread(this); - worker.start(); - - frame = new JInternalFrame(); - frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, - 100, false); - frame.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent evt) - { - ap.idPanel.idCanvas.setHighlighted(null); - } - } - ); - - } - - /** - * This is a copy of remove redundancy in jalivew.datamodel.Alignment - * except we dont want to remove redundancy, just calculate once - * so we can use the slider to dynamically hide redundant sequences - * - * @param threshold DOCUMENT ME! - * @param sel DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public void run() - { - JProgressBar progress = new JProgressBar(); - progress.setIndeterminate(true); - southPanel.add(progress, java.awt.BorderLayout.SOUTH); - - label.setText("Calculating...."); - - slider.setVisible(false); - applyButton.setEnabled(false); - valueField.setVisible(false); - - validate(); - - String[] omitHidden = null; - - SequenceGroup sg = ap.av.getSelectionGroup(); - int height; - - int start, end; - - if ( (sg != null) && (sg.getSize() >= 1)) - { - originalSequences = sg.getSequencesInOrder(ap.av.alignment); - start = sg.getStartRes(); - end = sg.getEndRes(); - } - else - { - originalSequences = ap.av.alignment.getSequencesArray(); - start = 0; - end = ap.av.alignment.getWidth(); - } - - height = originalSequences.length; - - redundancy = new float[height]; - for (int i = 0; i < height; i++) - { - redundancy[i] = 0f; - } - - if (ap.av.hasHiddenColumns) - { - omitHidden = ap.av.getViewAsString(sg != null); - } - - // long start = System.currentTimeMillis(); - - float pid; - String seqi, seqj; - for (int i = 0; i < height; i++) - { - - for (int j = 0; j < i; j++) - { - if (i == j) - { - continue; - } - - if (omitHidden == null) - { - seqi = originalSequences[i].getSequenceAsString(start, end); - seqj = originalSequences[j].getSequenceAsString(start, end); - } - else - { - seqi = omitHidden[i]; - seqj = omitHidden[j]; - } - - pid = Comparison.PID(seqi, seqj); - - if (seqj.length() < seqi.length()) - { - redundancy[j] = Math.max(pid, redundancy[j]); - } - else - { - redundancy[i] = Math.max(pid, redundancy[i]); - } - - } - } - - progress.setIndeterminate(false); - progress.setVisible(false); - progress = null; - - label.setText("Enter the redundancy threshold"); - slider.setVisible(true); - applyButton.setEnabled(true); - valueField.setVisible(true); - - validate(); - // System.out.println((System.currentTimeMillis()-start)); - } - - void sliderValueChanged() - { - if (redundancy == null) - { - return; - } - - float value = slider.getValue(); - - for (int i = 0; i < redundancy.length; i++) - { - if (value > redundancy[i]) - { - redundantSeqs.remove(originalSequences[i]); - } - else if (!redundantSeqs.contains(originalSequences[i])) - { - redundantSeqs.add(originalSequences[i]); - } - - } - - ap.idPanel.idCanvas.setHighlighted(redundantSeqs); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void applyButton_actionPerformed(ActionEvent e) - { - Vector del = new Vector(); - - undoButton.setEnabled(true); - - float value = slider.getValue(); - SequenceGroup sg = ap.av.getSelectionGroup(); - - for (int i = 0; i < redundancy.length; i++) - { - if (value <= redundancy[i]) - { - del.addElement(originalSequences[i]); - } - } - - // This has to be done before the restoreHistoryItem method of alignFrame will - // actually restore these sequences. - if (del.size() > 0) - { - SequenceI[] deleted = new SequenceI[del.size()]; - - int width = 0; - for (int i = 0; i < del.size(); i++) - { - deleted[i] = (SequenceI) del.elementAt(i); - if (deleted[i].getLength() > width) - { - width = deleted[i].getLength(); - } - } - - EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, - ap.av.alignment); - - for (int i = 0; i < del.size(); i++) - { - ap.av.alignment.deleteSequence(deleted[i]); - PaintRefresher.Refresh(this, - ap.av.getSequenceSetId(), - true, - true); - if (sg != null) - { - sg.deleteSequence(deleted[i], false); - } - } - - historyList.push(cut); - - ap.alignFrame.addHistoryItem(cut); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } - - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void undoButton_actionPerformed(ActionEvent e) - { - CommandI command = (CommandI) historyList.pop(); - command.undoCommand(); - - if (ap.av.historyList.contains(command)) - { - ap.av.historyList.remove(command); - af.updateEditMenuBar(); - } - - ap.paintAlignment(true); - - if (historyList.size() == 0) - { - undoButton.setEnabled(false); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void valueField_actionPerformed(ActionEvent e) - { - try - { - int i = Integer.parseInt(valueField.getText()); - slider.setValue(i); - } - catch (Exception ex) - { - valueField.setText(slider.getValue() + ""); - } - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +import java.util.*; + +import java.awt.event.*; +import javax.swing.*; +import javax.swing.event.*; + +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.jbgui.*; +import jalview.util.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class RedundancyPanel + extends GSliderPanel implements Runnable +{ + AlignFrame af; + AlignmentPanel ap; + Stack historyList = new Stack(); // simpler than synching with alignFrame. + float[] redundancy; + SequenceI[] originalSequences; + JInternalFrame frame; + Vector redundantSeqs; + + /** + * Creates a new RedundancyPanel object. + * + * @param ap DOCUMENT ME! + * @param af DOCUMENT ME! + */ + public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) + { + this.ap = ap; + this.af = af; + redundantSeqs = new Vector(); + + slider.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + valueField.setText(slider.getValue() + ""); + sliderValueChanged(); + } + }); + + applyButton.setText("Remove"); + allGroupsCheck.setVisible(false); + slider.setMinimum(0); + slider.setMaximum(100); + slider.setValue(100); + + Thread worker = new Thread(this); + worker.start(); + + frame = new JInternalFrame(); + frame.setContentPane(this); + Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, + 100, false); + frame.addInternalFrameListener(new InternalFrameAdapter() + { + public void internalFrameClosing(InternalFrameEvent evt) + { + ap.idPanel.idCanvas.setHighlighted(null); + } + } + ); + + } + + /** + * This is a copy of remove redundancy in jalivew.datamodel.Alignment + * except we dont want to remove redundancy, just calculate once + * so we can use the slider to dynamically hide redundant sequences + * + * @param threshold DOCUMENT ME! + * @param sel DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public void run() + { + JProgressBar progress = new JProgressBar(); + progress.setIndeterminate(true); + southPanel.add(progress, java.awt.BorderLayout.SOUTH); + + label.setText("Calculating...."); + + slider.setVisible(false); + applyButton.setEnabled(false); + valueField.setVisible(false); + + validate(); + + String[] omitHidden = null; + + SequenceGroup sg = ap.av.getSelectionGroup(); + int height; + + int start, end; + + if ( (sg != null) && (sg.getSize() >= 1)) + { + originalSequences = sg.getSequencesInOrder(ap.av.alignment); + start = sg.getStartRes(); + end = sg.getEndRes(); + } + else + { + originalSequences = ap.av.alignment.getSequencesArray(); + start = 0; + end = ap.av.alignment.getWidth(); + } + + height = originalSequences.length; + + redundancy = new float[height]; + for (int i = 0; i < height; i++) + { + redundancy[i] = 0f; + } + + if (ap.av.hasHiddenColumns) + { + omitHidden = ap.av.getViewAsString(sg != null); + } + + // long start = System.currentTimeMillis(); + + float pid; + String seqi, seqj; + for (int i = 0; i < height; i++) + { + + for (int j = 0; j < i; j++) + { + if (i == j) + { + continue; + } + + if (omitHidden == null) + { + seqi = originalSequences[i].getSequenceAsString(start, end); + seqj = originalSequences[j].getSequenceAsString(start, end); + } + else + { + seqi = omitHidden[i]; + seqj = omitHidden[j]; + } + + pid = Comparison.PID(seqi, seqj); + + if (seqj.length() < seqi.length()) + { + redundancy[j] = Math.max(pid, redundancy[j]); + } + else + { + redundancy[i] = Math.max(pid, redundancy[i]); + } + + } + } + + progress.setIndeterminate(false); + progress.setVisible(false); + progress = null; + + label.setText("Enter the redundancy threshold"); + slider.setVisible(true); + applyButton.setEnabled(true); + valueField.setVisible(true); + + validate(); + // System.out.println((System.currentTimeMillis()-start)); + } + + void sliderValueChanged() + { + if (redundancy == null) + { + return; + } + + float value = slider.getValue(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value > redundancy[i]) + { + redundantSeqs.remove(originalSequences[i]); + } + else if (!redundantSeqs.contains(originalSequences[i])) + { + redundantSeqs.add(originalSequences[i]); + } + + } + + ap.idPanel.idCanvas.setHighlighted(redundantSeqs); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void applyButton_actionPerformed(ActionEvent e) + { + Vector del = new Vector(); + + undoButton.setEnabled(true); + + float value = slider.getValue(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + for (int i = 0; i < redundancy.length; i++) + { + if (value <= redundancy[i]) + { + del.addElement(originalSequences[i]); + } + } + + // This has to be done before the restoreHistoryItem method of alignFrame will + // actually restore these sequences. + if (del.size() > 0) + { + SequenceI[] deleted = new SequenceI[del.size()]; + + int width = 0; + for (int i = 0; i < del.size(); i++) + { + deleted[i] = (SequenceI) del.elementAt(i); + if (deleted[i].getLength() > width) + { + width = deleted[i].getLength(); + } + } + + EditCommand cut = new EditCommand("Remove Redundancy", + EditCommand.CUT, deleted, 0, width, + ap.av.alignment); + + for (int i = 0; i < del.size(); i++) + { + ap.av.alignment.deleteSequence(deleted[i]); + PaintRefresher.Refresh(this, + ap.av.getSequenceSetId(), + true, + true); + if (sg != null) + { + sg.deleteSequence(deleted[i], false); + } + } + + historyList.push(cut); + + ap.alignFrame.addHistoryItem(cut); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void undoButton_actionPerformed(ActionEvent e) + { + CommandI command = (CommandI) historyList.pop(); + command.undoCommand(af.getViewAlignments()); + + if (ap.av.historyList.contains(command)) + { + ap.av.historyList.remove(command); + af.updateEditMenuBar(); + } + + ap.paintAlignment(true); + + if (historyList.size() == 0) + { + undoButton.setEnabled(false); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void valueField_actionPerformed(ActionEvent e) + { + try + { + int i = Integer.parseInt(valueField.getText()); + slider.setValue(i); + } + catch (Exception ex) + { + valueField.setText(slider.getValue() + ""); + } + } + +} -- 1.7.10.2