From 838aac5c22366a99df93de174971ff1ca016f417 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 5 May 2011 13:55:16 +0000 Subject: [PATCH] javadoc and informative error message when external binding to PDB fails --- src/jalview/appletgui/AlignFrame.java | 7135 +++++++++++++++++---------------- 1 file changed, 3575 insertions(+), 3560 deletions(-) diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index f7cfba0..4634142 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,3560 +1,3575 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . - */ -package jalview.appletgui; - -import java.net.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.api.SequenceStructureBinding; -import jalview.bin.JalviewLite; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; -import jalview.structure.StructureSelectionManager; - -public class AlignFrame extends EmbmenuFrame implements ActionListener, - ItemListener, KeyListener -{ - public AlignmentPanel alignPanel; - - public AlignViewport viewport; - - int DEFAULT_WIDTH = 700; - - int DEFAULT_HEIGHT = 500; - - String jalviewServletURL; - - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, - String title, boolean embedded) - { - - if (applet != null) - { - jalviewServletURL = applet.getParameter("APPLICATION_URL"); - } - - try - { - jbInit(); - } catch (Exception ex) - { - ex.printStackTrace(); - } - - viewport = new AlignViewport(al, applet); - alignPanel = new AlignmentPanel(this, viewport); - - viewport.updateConservation(alignPanel); - viewport.updateConsensus(alignPanel); - - annotationPanelMenuItem.setState(viewport.showAnnotation); - displayNonconservedMenuItem.setState(viewport.getShowunconserved()); - followMouseOverFlag.setState(viewport.getFollowHighlight()); - showGroupConsensus.setState(viewport.showGroupConsensus); - showGroupConservation.setState(viewport.showGroupConservation); - showConsensusHistogram.setState(viewport.showConsensusHistogram); - showSequenceLogo.setState(viewport.showSequenceLogo); - - seqLimits.setState(viewport.showJVSuffix); - - if (applet != null) - { - String param = applet.getParameter("sortBy"); - if (param != null) - { - if (param.equalsIgnoreCase("Id")) - { - sortIDMenuItem_actionPerformed(); - } - else if (param.equalsIgnoreCase("Pairwise Identity")) - { - sortPairwiseMenuItem_actionPerformed(); - } - else if (param.equalsIgnoreCase("Length")) - { - sortLengthMenuItem_actionPerformed(); - } - } - - param = applet.getParameter("wrap"); - if (param != null) - { - if (param.equalsIgnoreCase("true")) - { - wrapMenuItem.setState(true); - wrapMenuItem_actionPerformed(); - } - } - param = applet.getParameter("centrecolumnlabels"); - if (param != null) - { - centreColumnLabelFlag.setState(true); - centreColumnLabelFlag_stateChanged(); - } - try - { - param = applet.getParameter("windowWidth"); - if (param != null) - { - int width = Integer.parseInt(param); - DEFAULT_WIDTH = width; - } - param = applet.getParameter("windowHeight"); - if (param != null) - { - int height = Integer.parseInt(param); - DEFAULT_HEIGHT = height; - } - } catch (Exception ex) - { - } - - } - - // Some JVMS send keyevents to Top frame or lowest panel, - // Havent worked out why yet. So add to both this frame and seqCanvas for - // now - this.addKeyListener(this); - alignPanel.seqPanel.seqCanvas.addKeyListener(this); - alignPanel.idPanel.idCanvas.addKeyListener(this); - alignPanel.scalePanel.addKeyListener(this); - alignPanel.annotationPanel.addKeyListener(this); - alignPanel.annotationPanelHolder.addKeyListener(this); - alignPanel.annotationSpaceFillerHolder.addKeyListener(this); - alignPanel.alabels.addKeyListener(this); - createAlignFrameWindow(embedded, title); - alignPanel.validate(); - alignPanel.paintAlignment(true); - } - - public AlignViewport getAlignViewport() - { - return viewport; - } - - public SeqCanvas getSeqcanvas() - { - return alignPanel.seqPanel.seqCanvas; - } - - /** - * DOCUMENT ME! - * - * @param String - * DOCUMENT ME! - */ - - public void parseFeaturesFile(String file, String type) - { - Hashtable featureLinks = new Hashtable(); - boolean featuresFile = false; - try - { - featuresFile = new jalview.io.FeaturesFile(file, type) - .parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, - featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false)); - } catch (Exception ex) - { - ex.printStackTrace(); - } - - if (featuresFile) - { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; - } - viewport.showSequenceFeatures = true; - sequenceFeatures.setState(true); - if (viewport.featureSettings != null) - { - viewport.featureSettings.refreshTable(); - } - alignPanel.paintAlignment(true); - } - - } - - public void keyPressed(KeyEvent evt) - { - if (viewport.cursorMode - && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt - .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt - .getKeyCode() <= KeyEvent.VK_NUMPAD9)) - && Character.isDigit(evt.getKeyChar())) - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); - - switch (evt.getKeyCode()) - { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(); - - alignPanel.alabels.cancelDrag(); - break; - case KeyEvent.VK_X: - if (evt.isControlDown() || evt.isMetaDown()) - { - cut_actionPerformed(); - } - break; - case KeyEvent.VK_C: - if (viewport.cursorMode && !evt.isControlDown()) - { - alignPanel.seqPanel.setCursorColumn(); - } - if (evt.isControlDown() || evt.isMetaDown()) - { - copy_actionPerformed(); - } - break; - case KeyEvent.VK_V: - if (evt.isControlDown()) - { - paste(evt.isShiftDown()); - } - break; - case KeyEvent.VK_A: - if (evt.isControlDown() || evt.isMetaDown()) - { - selectAllSequenceMenuItem_actionPerformed(); - } - break; - case KeyEvent.VK_DOWN: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0, 1); - } - else - { - moveSelectedSequences(false); - } - break; - - case KeyEvent.VK_UP: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0, -1); - } - else - { - moveSelectedSequences(true); - } - break; - - case KeyEvent.VK_LEFT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor(-1, 0); - break; - - case KeyEvent.VK_RIGHT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor(1, 0); - break; - - case KeyEvent.VK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); - } - break; - - case KeyEvent.VK_DELETE: - case KeyEvent.VK_BACK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() - || evt.isShiftDown() || evt.isAltDown()); - } - else - { - cut_actionPerformed(); - alignPanel.seqPanel.seqCanvas.repaint(); - } - break; - - case KeyEvent.VK_S: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRow(); - } - break; - case KeyEvent.VK_P: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorPosition(); - } - break; - - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - break; - - case KeyEvent.VK_Q: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); - } - break; - case KeyEvent.VK_M: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); - } - break; - - case KeyEvent.VK_F2: - viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " - + (viewport.cursorMode ? "on" : "off")); - if (viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - break; - - case KeyEvent.VK_F: - if (evt.isControlDown()) - { - findMenuItem_actionPerformed(); - } - break; - - case KeyEvent.VK_H: - { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); - toggleHiddenRegions(toggleSeqs, toggleCols); - break; - } - - case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(true); - } - else - { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - - viewport.endSeq + viewport.startSeq); - } - break; - - case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } - break; - - case KeyEvent.VK_Z: - if (evt.isControlDown()) - { - undoMenuItem_actionPerformed(); - } - break; - - case KeyEvent.VK_Y: - if (evt.isControlDown()) - { - redoMenuItem_actionPerformed(); - } - break; - - case KeyEvent.VK_L: - if (evt.isControlDown()) - { - trimAlignment(true); - } - break; - - case KeyEvent.VK_R: - if (evt.isControlDown()) - { - trimAlignment(false); - } - break; - - case KeyEvent.VK_E: - if (evt.isControlDown()) - { - if (evt.isShiftDown()) - { - this.removeAllGapsMenuItem_actionPerformed(); - } - else - { - removeGappedColumnMenuItem_actionPerformed(); - } - } - break; - case KeyEvent.VK_I: - if (evt.isControlDown()) - { - if (evt.isAltDown()) - { - invertColSel_actionPerformed(); - } - else - { - invertSequenceMenuItem_actionPerformed(); - } - } - break; - - case KeyEvent.VK_U: - if (evt.isControlDown()) - { - this.deleteGroups_actionPerformed(); - } - break; - - case KeyEvent.VK_T: - if (evt.isControlDown()) - { - newView(null); - } - break; - - } - alignPanel.paintAlignment(true); - } - - /** - * called by key handler and the hide all/show all menu items - * - * @param toggleSeqs - * @param toggleCols - */ - private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) - { - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - if (!toggleSeqs && !toggleCols) - { - // Hide everything by the current selection - this is a hack - we do the - // invert and then hide - // first check that there will be visible columns after the invert. - if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel - .getSelected().size() > 0) - || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg - .getEndRes())) - { - // now invert the sequence set, if required - empty selection implies - // that no hiding is required. - if (sg != null) - { - invertSequenceMenuItem_actionPerformed(); - sg = viewport.getSelectionGroup(); - toggleSeqs = true; - - } - viewport.expandColSelection(sg, true); - // finally invert the column selection and get the new sequence - // selection and indicate it should be hidden. - invertColSel_actionPerformed(); - toggleCols = true; - } - } - - if (toggleSeqs) - { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hide = true; - viewport.hideAllSelectedSeqs(); - } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) - { - viewport.showAllHiddenSeqs(); - } - } - - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - viewport.hideSelectedColumns(); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - viewport.showAllHiddenColumns(); - } - } - } - - public void keyReleased(KeyEvent evt) - { - } - - public void keyTyped(KeyEvent evt) - { - } - - public void itemStateChanged(ItemEvent evt) - { - if (evt.getSource() == displayNonconservedMenuItem) - { - displayNonconservedMenuItem_actionPerformed(); - } - else if (evt.getSource() == colourTextMenuItem) - { - colourTextMenuItem_actionPerformed(); - } - else if (evt.getSource() == wrapMenuItem) - { - wrapMenuItem_actionPerformed(); - } - else if (evt.getSource() == scaleAbove) - { - viewport.setScaleAboveWrapped(scaleAbove.getState()); - } - else if (evt.getSource() == scaleLeft) - { - viewport.setScaleLeftWrapped(scaleLeft.getState()); - } - else if (evt.getSource() == scaleRight) - { - viewport.setScaleRightWrapped(scaleRight.getState()); - } - else if (evt.getSource() == seqLimits) - { - seqLimits_itemStateChanged(); - } - else if (evt.getSource() == viewBoxesMenuItem) - { - viewport.setShowBoxes(viewBoxesMenuItem.getState()); - } - else if (evt.getSource() == viewTextMenuItem) - { - viewport.setShowText(viewTextMenuItem.getState()); - } - else if (evt.getSource() == renderGapsMenuItem) - { - viewport.setRenderGaps(renderGapsMenuItem.getState()); - } - else if (evt.getSource() == annotationPanelMenuItem) - { - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); - } - else if (evt.getSource() == sequenceFeatures) - { - viewport.showSequenceFeatures(sequenceFeatures.getState()); - alignPanel.seqPanel.seqCanvas.repaint(); - } - else if (evt.getSource() == conservationMenuItem) - { - conservationMenuItem_actionPerformed(); - } - else if (evt.getSource() == abovePIDThreshold) - { - abovePIDThreshold_actionPerformed(); - } - else if (evt.getSource() == applyToAllGroups) - { - viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); - } - else if (evt.getSource() == autoCalculate) - { - viewport.autocalculateConsensus = autoCalculate.getState(); - } - else if (evt.getSource() == this.centreColumnLabelFlag) - { - centreColumnLabelFlag_stateChanged(); - } - else if (evt.getSource() == this.followMouseOverFlag) - { - mouseOverFlag_stateChanged(); - } - else if (evt.getSource() == showGroupConsensus) - { - showGroupConsensus_actionPerformed(); - } - else if (evt.getSource() == showGroupConservation) - { - showGroupConservation_actionPerformed(); - } - else if (evt.getSource() == showSequenceLogo) - { - showSequenceLogo_actionPerformed(); - } - else if (evt.getSource() == showConsensusHistogram) - { - showConsensusHistogram_actionPerformed(); - } - else if (evt.getSource() == applyAutoAnnotationSettings) - { - applyAutoAnnotationSettings_actionPerformed(); - } - alignPanel.paintAlignment(true); - } - - private void mouseOverFlag_stateChanged() - { - viewport.followHighlight = followMouseOverFlag.getState(); - // TODO: could kick the scrollTo mechanism to reset view for current - // searchresults. - } - - private void centreColumnLabelFlag_stateChanged() - { - viewport.centreColumnLabels = centreColumnLabelFlag.getState(); - this.alignPanel.annotationPanel.repaint(); - } - - public void actionPerformed(ActionEvent evt) - { - Object source = evt.getSource(); - - if (source == inputText) - { - inputText_actionPerformed(); - } - else if (source == loadTree) - { - loadTree_actionPerformed(); - } - else if (source == loadApplication) - { - launchFullApplication(); - } - else if (source == loadAnnotations) - { - loadAnnotations(); - } - else if (source == outputAnnotations) - { - outputAnnotations(true); - } - else if (source == outputFeatures) - { - outputFeatures(true, "Jalview"); - } - else if (source == closeMenuItem) - { - closeMenuItem_actionPerformed(); - } - else if (source == copy) - { - copy_actionPerformed(); - } - else if (source == undoMenuItem) - { - undoMenuItem_actionPerformed(); - } - else if (source == redoMenuItem) - { - redoMenuItem_actionPerformed(); - } - else if (source == inputText) - { - inputText_actionPerformed(); - } - else if (source == closeMenuItem) - { - closeMenuItem_actionPerformed(); - } - else if (source == undoMenuItem) - { - undoMenuItem_actionPerformed(); - } - else if (source == redoMenuItem) - { - redoMenuItem_actionPerformed(); - } - else if (source == copy) - { - copy_actionPerformed(); - } - else if (source == pasteNew) - { - pasteNew_actionPerformed(); - } - else if (source == pasteThis) - { - pasteThis_actionPerformed(); - } - else if (source == cut) - { - cut_actionPerformed(); - } - else if (source == delete) - { - delete_actionPerformed(); - } - else if (source == grpsFromSelection) - { - makeGrpsFromSelection_actionPerformed(); - } - else if (source == deleteGroups) - { - deleteGroups_actionPerformed(); - } - else if (source == selectAllSequenceMenuItem) - { - selectAllSequenceMenuItem_actionPerformed(); - } - else if (source == deselectAllSequenceMenuItem) - { - deselectAllSequenceMenuItem_actionPerformed(); - } - else if (source == invertSequenceMenuItem) - { - invertSequenceMenuItem_actionPerformed(); - } - else if (source == invertColSel) - { - viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); - } - else if (source == remove2LeftMenuItem) - { - trimAlignment(true); - } - else if (source == remove2RightMenuItem) - { - trimAlignment(false); - } - else if (source == removeGappedColumnMenuItem) - { - removeGappedColumnMenuItem_actionPerformed(); - } - else if (source == removeAllGapsMenuItem) - { - removeAllGapsMenuItem_actionPerformed(); - } - else if (source == findMenuItem) - { - findMenuItem_actionPerformed(); - } - else if (source == font) - { - new FontChooser(alignPanel); - } - else if (source == newView) - { - newView(null); - } - else if (source == showColumns) - { - viewport.showAllHiddenColumns(); - alignPanel.paintAlignment(true); - } - else if (source == showSeqs) - { - viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); - } - else if (source == hideColumns) - { - viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); - } - else if (source == hideSequences - && viewport.getSelectionGroup() != null) - { - viewport.hideAllSelectedSeqs(); - alignPanel.paintAlignment(true); - } - else if (source == hideAllButSelection) - { - toggleHiddenRegions(false, false); - alignPanel.paintAlignment(true); - } - else if (source == hideAllSelection) - { - SequenceGroup sg = viewport.getSelectionGroup(); - viewport.expandColSelection(sg, false); - viewport.hideAllSelectedSeqs(); - viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); - } - else if (source == showAllHidden) - { - viewport.showAllHiddenColumns(); - viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); - } - else if (source == showGroupConsensus) - { - showGroupConsensus_actionPerformed(); - } - else if (source == showGroupConservation) - { - showGroupConservation_actionPerformed(); - } - else if (source == showSequenceLogo) - { - showSequenceLogo_actionPerformed(); - } - else if (source == showConsensusHistogram) - { - showConsensusHistogram_actionPerformed(); - } - else if (source == applyAutoAnnotationSettings) - { - applyAutoAnnotationSettings_actionPerformed(); - } - else if (source == featureSettings) - { - new FeatureSettings(alignPanel); - } - else if (source == alProperties) - { - StringBuffer contents = new jalview.io.AlignmentProperties( - viewport.alignment).formatAsString(); - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - cap.setText(contents.toString()); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: " - + getTitle(), 400, 250); - } - else if (source == overviewMenuItem) - { - overviewMenuItem_actionPerformed(); - } - else if (source == noColourmenuItem) - { - changeColour(null); - } - else if (source == clustalColour) - { - abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), - viewport.alignment.getWidth())); - } - else if (source == zappoColour) - { - changeColour(new ZappoColourScheme()); - } - else if (source == taylorColour) - { - changeColour(new TaylorColourScheme()); - } - else if (source == hydrophobicityColour) - { - changeColour(new HydrophobicColourScheme()); - } - else if (source == helixColour) - { - changeColour(new HelixColourScheme()); - } - else if (source == strandColour) - { - changeColour(new StrandColourScheme()); - } - else if (source == turnColour) - { - changeColour(new TurnColourScheme()); - } - else if (source == buriedColour) - { - changeColour(new BuriedColourScheme()); - } - else if (source == nucleotideColour) - { - changeColour(new NucleotideColourScheme()); - } - else if (source == modifyPID) - { - modifyPID_actionPerformed(); - } - else if (source == modifyConservation) - { - modifyConservation_actionPerformed(); - } - else if (source == userDefinedColour) - { - new UserDefinedColours(alignPanel, null); - } - else if (source == PIDColour) - { - changeColour(new PIDColourScheme()); - } - else if (source == BLOSUM62Colour) - { - changeColour(new Blosum62ColourScheme()); - } - else if (source == annotationColour) - { - new AnnotationColourChooser(viewport, alignPanel); - } - else if (source == sortPairwiseMenuItem) - { - sortPairwiseMenuItem_actionPerformed(); - } - else if (source == sortIDMenuItem) - { - sortIDMenuItem_actionPerformed(); - } - else if (source == sortLengthMenuItem) - { - sortLengthMenuItem_actionPerformed(); - } - else if (source == sortGroupMenuItem) - { - sortGroupMenuItem_actionPerformed(); - } - else if (source == removeRedundancyMenuItem) - { - removeRedundancyMenuItem_actionPerformed(); - } - else if (source == pairwiseAlignmentMenuItem) - { - pairwiseAlignmentMenuItem_actionPerformed(); - } - else if (source == PCAMenuItem) - { - PCAMenuItem_actionPerformed(); - } - else if (source == averageDistanceTreeMenuItem) - { - averageDistanceTreeMenuItem_actionPerformed(); - } - else if (source == neighbourTreeMenuItem) - { - neighbourTreeMenuItem_actionPerformed(); - } - else if (source == njTreeBlosumMenuItem) - { - njTreeBlosumMenuItem_actionPerformed(); - } - else if (source == avDistanceTreeBlosumMenuItem) - { - avTreeBlosumMenuItem_actionPerformed(); - } - else if (source == documentation) - { - documentation_actionPerformed(); - } - else if (source == about) - { - about_actionPerformed(); - } - - } - - public void inputText_actionPerformed() - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); - } - - protected void outputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(new AppletFormatAdapter().formatSequences( - e.getActionCommand(), viewport.getAlignment(), - viewport.showJVSuffix)); - } - - public void loadAnnotations() - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your features / annotations file here."); - cap.setAnnotationImport(); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); - - } - - public String outputAnnotations(boolean displayTextbox) - { - String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); - - if (displayTextbox) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500); - cap.setText(annotation); - } - - return annotation; - } - - private Hashtable getDisplayedFeatureCols() - { - if (alignPanel.getFeatureRenderer() != null) - { - FeatureRenderer fr = alignPanel.getFeatureRenderer(); - Hashtable fcols = new Hashtable(); - Enumeration en = viewport.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); - } - return fcols; - } - return null; - } - - public String outputFeatures(boolean displayTextbox, String format) - { - String features; - if (format.equalsIgnoreCase("Jalview")) - { - features = new FeaturesFile().printJalviewFormat( - viewport.alignment.getSequencesArray(), - getDisplayedFeatureCols()); - } - else - { - features = new FeaturesFile().printGFFFormat( - viewport.alignment.getSequencesArray(), - getDisplayedFeatureCols()); - } - - if (displayTextbox) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); - - cap.setText(features); - } - - return features; - } - - void launchFullApplication() - { - StringBuffer url = new StringBuffer(jalviewServletURL); - - url.append("?open=" - + appendProtocol(viewport.applet.getParameter("file"))); - - if (viewport.applet.getParameter("features") != null) - { - url.append("&features="); - url.append(appendProtocol(viewport.applet.getParameter("features"))); - } - - if (viewport.applet.getParameter("annotations") != null) - { - url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("annotations"))); - } - - if (viewport.applet.getParameter("jnetfile") != null) - { - url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); - } - - if (viewport.applet.getParameter("defaultColour") != null) - { - url.append("&colour=" - + removeWhiteSpace(viewport.applet - .getParameter("defaultColour"))); - } - - if (viewport.applet.getParameter("userDefinedColour") != null) - { - url.append("&colour=" - + removeWhiteSpace(viewport.applet - .getParameter("userDefinedColour"))); - } - if (viewport.applet.getParameter("tree") != null) - { - url.append("&tree=" - + appendProtocol(viewport.applet.getParameter("tree"))); - } - if (viewport.applet.getParameter("treeFile") != null) - { - url.append("&tree=" - + appendProtocol(viewport.applet.getParameter("treeFile"))); - } - - showURL(url.toString(), "FULL_APP"); - } - - String removeWhiteSpace(String colour) - { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < colour.length(); i++) - { - if (Character.isWhitespace(colour.charAt(i))) - { - sb.append("%20"); - } - else - { - sb.append(colour.charAt(i)); - } - } - - return sb.toString(); - } - - String appendProtocol(String url) - { - try - { - new URL(url); - url = URLEncoder.encode(url); - } - /* - * When we finally deprecate 1.1 compatibility, we can start to use - * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch - * (UnsupportedEncodingException ex) { System.err.println("WARNING - - * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url); - * ex.printStackTrace(); } - */ - catch (java.net.MalformedURLException ex) - { - url = viewport.applet.getCodeBase() + url; - } - return url; - } - - public void closeMenuItem_actionPerformed() - { - PaintRefresher.RemoveComponent(alignPanel); - PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); - - if (PaintRefresher.components.size() == 0 && viewport.applet == null) - { - System.exit(0); - } - - this.dispose(); - } - - /** - * DOCUMENT ME! - */ - void updateEditMenuBar() - { - - if (viewport.historyList.size() > 0) - { - undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setLabel("Undo " + command.getDescription()); - } - else - { - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - } - - if (viewport.redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - - CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setLabel("Redo " + command.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - } - } - - public void addHistoryItem(CommandI command) - { - if (command.getSize() > 0) - { - viewport.historyList.push(command); - viewport.redoList.removeAllElements(); - updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - } - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void undoMenuItem_actionPerformed() - { - if (viewport.historyList.size() < 1) - { - return; - } - - CommandI command = (CommandI) viewport.historyList.pop(); - viewport.redoList.push(command); - command.undoCommand(null); - - AlignViewport originalSource = getOriginatingSource(command); - - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void redoMenuItem_actionPerformed() - { - if (viewport.redoList.size() < 1) - { - return; - } - - CommandI command = (CommandI) viewport.redoList.pop(); - viewport.historyList.push(command); - command.doCommand(null); - - AlignViewport originalSource = getOriginatingSource(command); - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; - - updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); - } - - AlignViewport getOriginatingSource(CommandI command) - { - AlignViewport originalSource = null; - // For sequence removal and addition, we need to fire - // the property change event FROM the viewport where the - // original alignment was altered - AlignmentI al = null; - if (command instanceof EditCommand) - { - EditCommand editCommand = (EditCommand) command; - al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components.get(viewport - .getSequenceSetId()); - for (int i = 0; i < comps.size(); i++) - { - if (comps.elementAt(i) instanceof AlignmentPanel) - { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) - { - originalSource = ((AlignmentPanel) comps.elementAt(i)).av; - break; - } - } - } - } - - if (originalSource == null) - { - // The original view is closed, we must validate - // the current view against the closed view first - if (al != null) - { - PaintRefresher.validateSequences(al, viewport.alignment); - } - - originalSource = viewport; - } - - return originalSource; - } - - public void moveSelectedSequences(boolean up) - { - SequenceGroup sg = viewport.getSelectionGroup(); - if (sg == null) - { - return; - } - - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - - alignPanel.paintAlignment(true); - } - - synchronized void slideSequences(boolean right, int size) - { - Vector sg = new Vector(); - if (viewport.cursorMode) - { - sg.addElement(viewport.alignment - .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); - } - else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment - .getHeight()) - { - sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); - } - - if (sg.size() < 1) - { - return; - } - - Vector invertGroup = new Vector(); - - for (int i = 0; i < viewport.alignment.getHeight(); i++) - { - if (!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.addElement(viewport.alignment.getSequenceAt(i)); - } - - SequenceI[] seqs1 = new SequenceI[sg.size()]; - for (int i = 0; i < sg.size(); i++) - seqs1[i] = (SequenceI) sg.elementAt(i); - - SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; - for (int i = 0; i < invertGroup.size(); i++) - seqs2[i] = (SequenceI) invertGroup.elementAt(i); - - SlideSequencesCommand ssc; - if (right) - ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, - size, viewport.getGapCharacter()); - else - ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, - size, viewport.getGapCharacter()); - - int groupAdjustment = 0; - if (ssc.getGapsInsertedBegin() && right) - { - if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(size, 0); - else - groupAdjustment = size; - } - else if (!ssc.getGapsInsertedBegin() && !right) - { - if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(-size, 0); - else - groupAdjustment = -size; - } - - if (groupAdjustment != 0) - { - viewport.getSelectionGroup().setStartRes( - viewport.getSelectionGroup().getStartRes() + groupAdjustment); - viewport.getSelectionGroup().setEndRes( - viewport.getSelectionGroup().getEndRes() + groupAdjustment); - } - - boolean appendHistoryItem = false; - if (viewport.historyList != null && viewport.historyList.size() > 0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) - { - appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) viewport.historyList - .peek()); - } - - if (!appendHistoryItem) - addHistoryItem(ssc); - - repaint(); - } - - static StringBuffer copiedSequences; - - static Vector copiedHiddenColumns; - - protected void copy_actionPerformed() - { - if (viewport.getSelectionGroup() == null) - { - return; - } - - SequenceGroup sg = viewport.getSelectionGroup(); - copiedSequences = new StringBuffer(); - Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); - orderedSeqs.put(index + "", seq); - } - - int index = 0, startRes, endRes; - char ch; - - if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) - { - copiedHiddenColumns = new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) - { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); - - copiedHiddenColumns.addElement(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); - } - } - else - { - copiedHiddenColumns = null; - } - - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = null; - - while (seq == null) - { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; - - break; - } - else - { - index++; - } - } - - // FIND START RES - // Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); - - // FIND END RES - // Need to find the residue preceeding index if gap - endRes = 0; - - for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) - { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap((ch))) - { - endRes++; - } - } - - if (endRes > 0) - { - endRes += seq.getStart() - 1; - } - - copiedSequences.append(seq.getName() - + "\t" - + startRes - + "\t" - + endRes - + "\t" - + seq.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); - } - - } - - protected void pasteNew_actionPerformed() - { - paste(true); - } - - protected void pasteThis_actionPerformed() - { - paste(false); - } - - void paste(boolean newAlignment) - { - try - { - - if (copiedSequences == null) - { - return; - } - - StringTokenizer st = new StringTokenizer(copiedSequences.toString()); - Vector seqs = new Vector(); - while (st.hasMoreElements()) - { - String name = st.nextToken(); - int start = Integer.parseInt(st.nextToken()); - int end = Integer.parseInt(st.nextToken()); - seqs.addElement(new Sequence(name, st.nextToken(), start, end)); - } - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - - if (newAlignment) - { - String newtitle = new String("Copied sequences"); - if (getTitle().startsWith("Copied sequences")) - { - newtitle = getTitle(); - } - else - { - newtitle = newtitle.concat("- from " + getTitle()); - } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), - viewport.applet, newtitle, false); - if (copiedHiddenColumns != null) - { - for (int i = 0; i < copiedHiddenColumns.size(); i++) - { - int[] region = (int[]) copiedHiddenColumns.elementAt(i); - af.viewport.hideColumns(region[0], region[1]); - } - } - - jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } - else - { - addSequences(newSeqs); - } - - } catch (Exception ex) - { - } // could be anything being pasted in here - - } - - void addSequences(SequenceI[] seqs) - { - for (int i = 0; i < seqs.length; i++) - { - viewport.alignment.addSequence(seqs[i]); - } - - // !newAlignment - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, - seqs, 0, viewport.alignment.getWidth(), viewport.alignment)); - - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, - viewport.alignment.getSequences()); - - } - - protected void cut_actionPerformed() - { - copy_actionPerformed(); - delete_actionPerformed(); - } - - protected void delete_actionPerformed() - { - - SequenceGroup sg = viewport.getSelectionGroup(); - if (sg == null) - { - return; - } - - Vector seqs = new Vector(); - SequenceI seq; - for (int i = 0; i < sg.getSize(); i++) - { - seq = sg.getSequenceAt(i); - seqs.addElement(seq); - } - - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - - SequenceI[] cut = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - cut[i] = (SequenceI) seqs.elementAt(i); - } - - /* - * //ADD HISTORY ITEM - */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); - - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); - - if (viewport.getAlignment().getHeight() < 1) - { - this.setVisible(false); - } - viewport.sendSelection(); - } - - /** - * group consensus toggled - * - */ - protected void showGroupConsensus_actionPerformed() - { - viewport.setShowGroupConsensus(showGroupConsensus.getState()); - alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - - } - - /** - * group conservation toggled. - */ - protected void showGroupConservation_actionPerformed() - { - viewport.setShowGroupConservation(showGroupConservation.getState()); - alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt - * .event.ActionEvent) - */ - protected void showConsensusHistogram_actionPerformed() - { - viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); - alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - } - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt - * .event.ActionEvent) - */ - protected void showSequenceLogo_actionPerformed() - { - viewport.setShowSequenceLogo(showSequenceLogo.getState()); - alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - } - - protected void applyAutoAnnotationSettings_actionPerformed() - { - alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); - } - - protected void makeGrpsFromSelection_actionPerformed() - { - if (viewport.getSelectionGroup() != null) - { - SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( - viewport.getSequenceSelection(), - viewport.getAlignmentView(true).getSequenceStrings( - viewport.getGapCharacter()), - viewport.alignment.getGroups()); - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - // set view properties for each group - for (int g = 0; g < gps.length; g++) - { - // gps[g].setShowunconserved(viewport.getShowUnconserved()); - gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); - viewport.alignment.addGroup(gps[g]); - Color col = new Color((int) (Math.random() * 255), - (int) (Math.random() * 255), (int) (Math.random() * 255)); - col = col.brighter(); - for (Enumeration sq = gps[g].getSequences(null).elements(); sq - .hasMoreElements(); viewport.setSequenceColour( - (SequenceI) sq.nextElement(), col)) - ; - } - PaintRefresher.Refresh(this, viewport.getSequenceSetId()); - alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); - } - } - - protected void deleteGroups_actionPerformed() - { - viewport.alignment.deleteAllGroups(); - viewport.sequenceColours = null; - viewport.setSelectionGroup(null); - - alignPanel.paintAlignment(true); - } - - public void selectAllSequenceMenuItem_actionPerformed() - { - SequenceGroup sg = new SequenceGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); - } - sg.setEndRes(viewport.alignment.getWidth() - 1); - viewport.setSelectionGroup(sg); - alignPanel.paintAlignment(true); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); - } - - public void deselectAllSequenceMenuItem_actionPerformed() - { - if (viewport.cursorMode) - { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.idPanel.idCanvas.searchResults = null; - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.paintAlignment(true); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); - } - - public void invertSequenceMenuItem_actionPerformed() - { - SequenceGroup sg = viewport.getSelectionGroup(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } - - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); - } - - public void invertColSel_actionPerformed() - { - viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); - PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); - viewport.sendSelection(); - } - - void trimAlignment(boolean trimLeft) - { - ColumnSelection colSel = viewport.getColumnSelection(); - int column; - - if (colSel.size() > 0) - { - if (trimLeft) - { - column = colSel.getMin(); - } - else - { - column = colSel.getMax(); - } - - SequenceI[] seqs; - if (viewport.getSelectionGroup() != null) - { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); - } - else - { - seqs = viewport.alignment.getSequencesArray(); - } - - TrimRegionCommand trimRegion; - if (trimLeft) - { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); - viewport.setStartRes(0); - } - else - { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); - } - - statusBar.setText("Removed " + trimRegion.getSize() + " columns."); - - addHistoryItem(trimRegion); - - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if ((trimLeft && !sg.adjustForRemoveLeft(column)) - || (!trimLeft && !sg.adjustForRemoveRight(column))) - { - viewport.alignment.deleteGroup(sg); - } - } - - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); - } - } - - public void removeGappedColumnMenuItem_actionPerformed() - { - int start = 0, end = viewport.alignment.getWidth() - 1; - - SequenceI[] seqs; - if (viewport.getSelectionGroup() != null) - { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); - } - else - { - seqs = viewport.alignment.getSequencesArray(); - } - - RemoveGapColCommand removeGapCols = new RemoveGapColCommand( - "Remove Gapped Columns", seqs, start, end, viewport.alignment); - - addHistoryItem(removeGapCols); - - statusBar.setText("Removed " + removeGapCols.getSize() - + " empty columns."); - - // This is to maintain viewport position on first residue - // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - // ShiftList shifts; - // viewport.getAlignment().removeGaps(shifts=new ShiftList()); - // edit.alColumnChanges=shifts.getInverse(); - // if (viewport.hasHiddenColumns) - // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); - - } - - public void removeAllGapsMenuItem_actionPerformed() - { - int start = 0, end = viewport.alignment.getWidth() - 1; - - SequenceI[] seqs; - if (viewport.getSelectionGroup() != null) - { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); - } - else - { - seqs = viewport.alignment.getSequencesArray(); - } - - // This is to maintain viewport position on first residue - // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.alignment)); - - viewport.setStartRes(seq.findIndex(startRes) - 1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); - - } - - public void findMenuItem_actionPerformed() - { - new Finder(alignPanel); - } - - /** - * create a new view derived from the current view - * - * @param viewtitle - * @return frame for the new view - */ - public AlignFrame newView(String viewtitle) - { - AlignmentI newal; - if (viewport.hasHiddenRows) - { - newal = new Alignment(viewport.getAlignment().getHiddenSequences() - .getFullAlignment().getSequencesArray()); - } - else - { - newal = new Alignment(viewport.alignment.getSequencesArray()); - } - - if (viewport.alignment.getAlignmentAnnotation() != null) - { - for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) - { - if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) - { - newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); - } - } - } - - AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); - - newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); - PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); - PaintRefresher.Register(newaf.alignPanel, - newaf.alignPanel.av.getSequenceSetId()); - - PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, - newaf.alignPanel.av.getSequenceSetId()); - PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, - newaf.alignPanel.av.getSequenceSetId()); - - Vector comps = (Vector) PaintRefresher.components.get(viewport - .getSequenceSetId()); - int viewSize = -1; - for (int i = 0; i < comps.size(); i++) - { - if (comps.elementAt(i) instanceof AlignmentPanel) - { - viewSize++; - } - } - - String title = new String(this.getTitle()); - if (viewtitle != null) - { - title = viewtitle + " ( " + title + ")"; - } - else - { - if (title.indexOf("(View") > -1) - { - title = title.substring(0, title.indexOf("(View")); - } - title += "(View " + viewSize + ")"; - } - - newaf.setTitle(title.toString()); - - newaf.viewport.historyList = viewport.historyList; - newaf.viewport.redoList = viewport.redoList; - return newaf; - } - - /** - * - * @return list of feature groups on the view - */ - public String[] getFeatureGroups() - { - FeatureRenderer fr = null; - if (alignPanel != null - && (fr = alignPanel.getFeatureRenderer()) != null) - { - return fr.getGroups(); - } - return null; - } - - /** - * get sequence feature groups that are hidden or shown - * - * @param visible - * true is visible - * @return list - */ - public String[] getFeatureGroupsOfState(boolean visible) - { - FeatureRenderer fr = null; - if (alignPanel != null - && (fr = alignPanel.getFeatureRenderer()) != null) - { - return fr.getGroups(visible); - } - return null; - } - - /** - * Change the display state for the given feature groups - * - * @param groups - * list of group strings - * @param state - * visible or invisible - */ - public void setFeatureGroupState(String[] groups, boolean state) - { - FeatureRenderer fr = null; - this.sequenceFeatures.setState(true); - viewport.showSequenceFeatures(true); - if (alignPanel != null - && (fr = alignPanel.getFeatureRenderer()) != null) - { - fr.setGroupState(groups, state); - alignPanel.seqPanel.seqCanvas.repaint(); - if (alignPanel.overviewPanel != null) - { - alignPanel.overviewPanel.updateOverviewImage(); - } - } - } - - public void seqLimits_itemStateChanged() - { - viewport.setShowJVSuffix(seqLimits.getState()); - alignPanel.fontChanged(); - alignPanel.paintAlignment(true); - } - - protected void colourTextMenuItem_actionPerformed() - { - viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.paintAlignment(true); - } - - protected void displayNonconservedMenuItem_actionPerformed() - { - viewport.setShowunconserved(displayNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); - } - - protected void wrapMenuItem_actionPerformed() - { - viewport.setWrapAlignment(wrapMenuItem.getState()); - alignPanel.setWrapAlignment(wrapMenuItem.getState()); - scaleAbove.setEnabled(wrapMenuItem.getState()); - scaleLeft.setEnabled(wrapMenuItem.getState()); - scaleRight.setEnabled(wrapMenuItem.getState()); - alignPanel.paintAlignment(true); - } - - public void overviewMenuItem_actionPerformed() - { - if (alignPanel.overviewPanel != null) - { - return; - } - - Frame frame = new Frame(); - OverviewPanel overview = new OverviewPanel(alignPanel); - frame.add(overview); - // +50 must allow for applet frame window - jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.getPreferredSize().width, - overview.getPreferredSize().height + 50); - - frame.pack(); - frame.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - alignPanel.setOverviewPanel(null); - }; - }); - - alignPanel.setOverviewPanel(overview); - - } - - void changeColour(ColourSchemeI cs) - { - int threshold = 0; - - if (cs != null) - { - if (viewport.getAbovePIDThreshold()) - { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); - - cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - - viewport.setGlobalColourScheme(cs); - } - else - { - cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); - - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - cs.setConservation(c); - - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - - } - else - { - cs.setConservation(null); - } - - cs.setConsensus(viewport.hconsensus); - - } - viewport.setGlobalColourScheme(cs); - - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (cs == null) - { - sg.cs = null; - continue; - } - if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), - sg.getWidth()); - } - else - { - try - { - sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } catch (Exception ex) - { - ex.printStackTrace(); - sg.cs = cs; - } - } - - if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) - { - sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), 0, - sg.getWidth())); - } - else - { - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport.hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - sg.cs.setConservation(c); - } - else - { - sg.cs.setConservation(null); - sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - } - - } - } - - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged( - alignPanel); - - alignPanel.paintAlignment(true); - } - - protected void modifyPID_actionPerformed() - { - if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } - } - - protected void modifyConservation_actionPerformed() - { - if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); - SliderPanel.showConservationSlider(); - } - } - - protected void conservationMenuItem_actionPerformed() - { - viewport.setConservationSelected(conservationMenuItem.getState()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(); - } - - public void abovePIDThreshold_actionPerformed() - { - viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); - - conservationMenuItem.setState(false); - viewport.setConservationSelected(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(); - } - - public void sortPairwiseMenuItem_actionPerformed() - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0), null); - - addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); - } - - public void sortIDMenuItem_actionPerformed() - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); - alignPanel.paintAlignment(true); - } - - public void sortLengthMenuItem_actionPerformed() - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByLength(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Length Sort", oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); - } - - public void sortGroupMenuItem_actionPerformed() - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByGroup(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); - - } - - public void removeRedundancyMenuItem_actionPerformed() - { - new RedundancyPanel(alignPanel); - } - - public void pairwiseAlignmentMenuItem_actionPerformed() - { - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() > 1) - { - Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, - 500); - } - } - - public void PCAMenuItem_actionPerformed() - { - // are the sequences aligned? - if (!viewport.alignment.isAligned(false)) - { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } - } - alignPanel.paintAlignment(true); - } - - if ((viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() < 4 && viewport - .getSelectionGroup().getSize() > 0) - || viewport.getAlignment().getHeight() < 4) - { - return; - } - - try - { - new PCAPanel(viewport); - } catch (java.lang.OutOfMemoryError ex) - { - } - - } - - public void averageDistanceTreeMenuItem_actionPerformed() - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - public void neighbourTreeMenuItem_actionPerformed() - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - protected void njTreeBlosumMenuItem_actionPerformed() - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - protected void avTreeBlosumMenuItem_actionPerformed() - { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } - - void NewTreePanel(String type, String pwType, String title) - { - // are the sequences aligned? - if (!viewport.alignment.isAligned(false)) - { - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) - { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } - } - alignPanel.paintAlignment(true); - - } - - if ((viewport.getSelectionGroup() != null && viewport - .getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null && viewport.alignment - .getHeight() > 1)) - { - final TreePanel tp = new TreePanel(alignPanel, type, pwType); - - addTreeMenuItem(tp, title); - - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); - } - } - - void loadTree_actionPerformed() - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your Newick tree file here."); - cap.setTreeImport(); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); - } - - public void loadTree(jalview.io.NewickFile tree, String treeFile) - { - TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); - } - - /** - * sort the alignment using the given treePanel - * - * @param treePanel - * tree used to sort view - * @param title - * string used for undo event name - */ - public void sortByTree(TreePanel treePanel, String title) - { - SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter - .sortByTree(viewport.getAlignment(), treePanel.getTree()); - // addHistoryItem(new HistoryItem("Sort", viewport.alignment, - // HistoryItem.SORT)); - addHistoryItem(new OrderCommand("Order by " + title, oldOrder, - viewport.alignment)); - alignPanel.paintAlignment(true); - } - - /** - * Do any automatic reordering of the alignment and add the necessary bits to - * the menu structure for the new tree - * - * @param treePanel - * @param title - */ - protected void addTreeMenuItem(final TreePanel treePanel, - final String title) - { - final MenuItem item = new MenuItem(title); - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - sortByTree(treePanel, title); // treePanel.getTitle()); - } - }); - - treePanel.addWindowListener(new WindowAdapter() - { - public void windowOpened(WindowEvent e) - { - if (viewport.sortByTree) - { - sortByTree(treePanel, title); - } - super.windowOpened(e); - } - - public void windowClosing(WindowEvent e) - { - sortByTreeMenu.remove(item); - }; - }); - } - public boolean sortBy(AlignmentOrder alorder, String undoname) - { - SequenceI[] oldOrder = viewport.getAlignment() - .getSequencesArray(); - if (viewport.applet.debug) - { - System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'"); - } - AlignmentSorter.sortBy(viewport.getAlignment(), alorder); - if (undoname!=null) - { - addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment)); - } - alignPanel.paintAlignment(true); - return true; - } - protected void documentation_actionPerformed() - { - showURL("http://www.jalview.org/help.html", "HELP"); - } - - protected void about_actionPerformed() - { - - class AboutPanel extends Canvas - { - String version; - - String builddate; - - public AboutPanel(String version, String builddate) - { - this.version = version; - this.builddate = builddate; - } - - public void paint(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getSize().width, getSize().height); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - FontMetrics fm = g.getFontMetrics(); - int fh = fm.getHeight(); - int y = 5, x = 7; - g.setColor(Color.black); - // TODO: update this text for each release or centrally store it for - // lite and application - g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("JalviewLite - Release " + version, x, y += fh); - g.setFont(new Font("Helvetica", Font.BOLD, 12)); - g.drawString("Build date: " + builddate, x, y += fh); - g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString( - "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,", - x, y += fh * 1.5); - g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); - g.drawString( - "Development managed by The Barton Group, University of Dundee, Scotland, UK.", - x, y += fh); - g.drawString( - "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", - x, y += fh); - g.drawString("If you use Jalview, please cite:", x, y += fh + 8); - g.drawString( - "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)", - x, y += fh); - g.drawString( - "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench", - x, y += fh); - g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033", - x, y += fh); - } - } - - Frame frame = new Frame(); - frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite - .getBuildDate())); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); - - } - - public void showURL(String url, String target) - { - if (viewport.applet == null) - { - System.out.println("Not running as applet - no browser available."); - } - else - { - try - { - if (url.indexOf(":") == -1) - { - // TODO: verify (Bas Vroling bug) prepend codebase or server URL to - // form valid URL - if (url.indexOf("/") == 0) - { - String codebase = viewport.applet.getCodeBase().toString(); - url = codebase.substring(0, codebase.length() - - viewport.applet.getCodeBase().getFile().length()) - + url; - } - else - { - url = viewport.applet.getCodeBase() + url; - } - System.out.println("Show url (prepended codebase): " + url); - } - else - { - System.out.println("Show url: " + url); - } - if (url.indexOf("javascript:") == 0) - { - // no target for the javascript context - viewport.applet.getAppletContext().showDocument( - new java.net.URL(url)); - } - else - { - viewport.applet.getAppletContext().showDocument( - new java.net.URL(url), target); - } - } catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - // //////////////////////////////////////////////////////////////////////////////// - // JBuilder Graphics here - - MenuBar alignFrameMenuBar = new MenuBar(); - - Menu fileMenu = new Menu("File"); - - MenuItem loadApplication = new MenuItem("View in Full Application"); - - MenuItem loadTree = new MenuItem("Load Associated Tree ..."); - - MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); - - MenuItem outputFeatures = new MenuItem("Export Features ..."); - - MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); - - MenuItem closeMenuItem = new MenuItem("Close"); - - Menu editMenu = new Menu("Edit"); - - Menu viewMenu = new Menu("View"); - - Menu colourMenu = new Menu("Colour"); - - Menu calculateMenu = new Menu("Calculate"); - - MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - - MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - - MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - - MenuItem remove2LeftMenuItem = new MenuItem(); - - MenuItem remove2RightMenuItem = new MenuItem(); - - MenuItem removeGappedColumnMenuItem = new MenuItem(); - - MenuItem removeAllGapsMenuItem = new MenuItem(); - - CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - - CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - - MenuItem sortPairwiseMenuItem = new MenuItem(); - - MenuItem sortIDMenuItem = new MenuItem(); - - MenuItem sortLengthMenuItem = new MenuItem(); - - MenuItem sortGroupMenuItem = new MenuItem(); - - MenuItem removeRedundancyMenuItem = new MenuItem(); - - MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - - MenuItem PCAMenuItem = new MenuItem(); - - MenuItem averageDistanceTreeMenuItem = new MenuItem(); - - MenuItem neighbourTreeMenuItem = new MenuItem(); - - BorderLayout borderLayout1 = new BorderLayout(); - - public Label statusBar = new Label(); - - Menu outputTextboxMenu = new Menu(); - - MenuItem clustalColour = new MenuItem(); - - MenuItem zappoColour = new MenuItem(); - - MenuItem taylorColour = new MenuItem(); - - MenuItem hydrophobicityColour = new MenuItem(); - - MenuItem helixColour = new MenuItem(); - - MenuItem strandColour = new MenuItem(); - - MenuItem turnColour = new MenuItem(); - - MenuItem buriedColour = new MenuItem(); - - MenuItem userDefinedColour = new MenuItem(); - - MenuItem PIDColour = new MenuItem(); - - MenuItem BLOSUM62Colour = new MenuItem(); - - MenuItem njTreeBlosumMenuItem = new MenuItem(); - - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - - CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - - CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - - CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); - - MenuItem alProperties = new MenuItem("Alignment Properties..."); - - MenuItem overviewMenuItem = new MenuItem(); - - MenuItem undoMenuItem = new MenuItem(); - - MenuItem redoMenuItem = new MenuItem(); - - CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - - MenuItem noColourmenuItem = new MenuItem(); - - CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - - CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - - MenuItem findMenuItem = new MenuItem(); - - CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - - MenuItem nucleotideColour = new MenuItem(); - - MenuItem deleteGroups = new MenuItem(); - - MenuItem grpsFromSelection = new MenuItem(); - - MenuItem delete = new MenuItem(); - - MenuItem copy = new MenuItem(); - - MenuItem cut = new MenuItem(); - - Menu pasteMenu = new Menu(); - - MenuItem pasteNew = new MenuItem(); - - MenuItem pasteThis = new MenuItem(); - - CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - - MenuItem font = new MenuItem(); - - CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - - CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - - CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - - MenuItem modifyPID = new MenuItem(); - - MenuItem modifyConservation = new MenuItem(); - - CheckboxMenuItem autoCalculate = new CheckboxMenuItem( - "Autocalculate Consensus", true); - - Menu sortByTreeMenu = new Menu(); - - Menu sort = new Menu(); - - Menu calculate = new Menu(); - - MenuItem inputText = new MenuItem(); - - Menu helpMenu = new Menu(); - - MenuItem documentation = new MenuItem(); - - MenuItem about = new MenuItem(); - - CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - - CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); - - CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); - Menu autoAnnMenu=new Menu(); - CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem(); - CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); - CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); - CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); - CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); - - private void jbInit() throws Exception - { - - setMenuBar(alignFrameMenuBar); - - MenuItem item; - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) - { - - item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); - - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add(item); - } - closeMenuItem.addActionListener(this); - loadApplication.addActionListener(this); - - loadTree.addActionListener(this); - loadAnnotations.addActionListener(this); - outputFeatures.addActionListener(this); - outputAnnotations.addActionListener(this); - selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(this); - sortLengthMenuItem.setLabel("by Length"); - sortLengthMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem - .setLabel("Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem - .setLabel("Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(this); - displayNonconservedMenuItem.setLabel("Show nonconserved"); - displayNonconservedMenuItem.addItemListener(this); - alProperties.addActionListener(this); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(this); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(this); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(this); - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - grpsFromSelection.setLabel("Make Groups for selection"); - grpsFromSelection.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - centreColumnLabelFlag.setLabel("Centre column labels"); - centreColumnLabelFlag.addItemListener(this); - followMouseOverFlag.setLabel("Automatic Scrolling"); - followMouseOverFlag.addItemListener(this); - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); - seqLimits.setLabel("Show Sequence Limits"); - seqLimits.addItemListener(this); - featureSettings.setLabel("Feature Settings..."); - featureSettings.addActionListener(this); - sequenceFeatures.setLabel("Sequence Features"); - sequenceFeatures.addItemListener(this); - sequenceFeatures.setState(false); - annotationColour.setLabel("by Annotation..."); - annotationColour.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Sequence Selection"); - invertColSel.setLabel("Invert Column Selection"); - menu1.setLabel("Show"); - showColumns.setLabel("All Columns "); - showSeqs.setLabel("All Sequences"); - menu2.setLabel("Hide"); - hideColumns.setLabel("Selected Columns"); - hideSequences.setLabel("Selected Sequences"); - hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)"); - hideAllSelection.setLabel("Selected Region"); - showAllHidden.setLabel("All Sequences and Columns"); - showGroupConsensus.setLabel("Group Consensus"); - showGroupConservation.setLabel("Group Conservation"); - showConsensusHistogram.setLabel("Show Consensus Histogram"); - showSequenceLogo.setLabel("Show Consensus Logo"); - applyAutoAnnotationSettings.setLabel("Apply to all groups"); - applyAutoAnnotationSettings.setState(true); - autoAnnMenu.setLabel("Autocalculated Annotation"); - - invertColSel.addActionListener(this); - showColumns.addActionListener(this); - showSeqs.addActionListener(this); - hideColumns.addActionListener(this); - hideSequences.addActionListener(this); - hideAllButSelection.addActionListener(this); - hideAllSelection.addActionListener(this); - showAllHidden.addActionListener(this); - showGroupConsensus.addItemListener(this); - showGroupConservation.addItemListener(this); - showConsensusHistogram.addItemListener(this); - showSequenceLogo.addItemListener(this); - applyAutoAnnotationSettings.addItemListener(this); - formatMenu.setLabel("Format"); - selectMenu.setLabel("Select"); - newView.setLabel("New View"); - newView.addActionListener(this); - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(selectMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(formatMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - - fileMenu.add(inputText); - fileMenu.add(loadTree); - fileMenu.add(loadAnnotations); - - fileMenu.addSeparator(); - fileMenu.add(outputTextboxMenu); - fileMenu.add(outputFeatures); - fileMenu.add(outputAnnotations); - - if (jalviewServletURL != null) - { - fileMenu.add(loadApplication); - } - - fileMenu.addSeparator(); - fileMenu.add(closeMenuItem); - - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(pasteMenu); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - viewMenu.add(newView); - viewMenu.addSeparator(); - viewMenu.add(menu1); - viewMenu.add(menu2); - viewMenu.addSeparator(); - viewMenu.add(followMouseOverFlag); - viewMenu.add(annotationPanelMenuItem); - autoAnnMenu.add(applyAutoAnnotationSettings); - autoAnnMenu.add(showConsensusHistogram); - autoAnnMenu.add(showSequenceLogo); - autoAnnMenu.addSeparator(); - autoAnnMenu.add(showGroupConservation); - autoAnnMenu.add(showGroupConsensus); - viewMenu.add(autoAnnMenu); - viewMenu.addSeparator(); - viewMenu.add(sequenceFeatures); - viewMenu.add(featureSettings); - viewMenu.addSeparator(); - viewMenu.add(alProperties); - viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.add(autoCalculate); - this.add(statusBar, BorderLayout.SOUTH); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortLengthMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - menu1.add(showColumns); - menu1.add(showSeqs); - menu1.add(showAllHidden); - menu2.add(hideColumns); - menu2.add(hideSequences); - menu2.add(hideAllSelection); - menu2.add(hideAllButSelection); - formatMenu.add(font); - formatMenu.add(seqLimits); - formatMenu.add(wrapMenuItem); - formatMenu.add(scaleAbove); - formatMenu.add(scaleLeft); - formatMenu.add(scaleRight); - formatMenu.add(viewBoxesMenuItem); - formatMenu.add(viewTextMenuItem); - formatMenu.add(colourTextMenuItem); - formatMenu.add(displayNonconservedMenuItem); - formatMenu.add(renderGapsMenuItem); - formatMenu.add(centreColumnLabelFlag); - selectMenu.add(findMenuItem); - selectMenu.addSeparator(); - selectMenu.add(selectAllSequenceMenuItem); - selectMenu.add(deselectAllSequenceMenuItem); - selectMenu.add(invertSequenceMenuItem); - selectMenu.add(invertColSel); - selectMenu.add(grpsFromSelection); - selectMenu.add(deleteGroups); - - } - - MenuItem featureSettings = new MenuItem(); - - CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); - - MenuItem annotationColour = new MenuItem(); - - MenuItem invertColSel = new MenuItem(); - - Menu menu1 = new Menu(); - - MenuItem showColumns = new MenuItem(); - - MenuItem showSeqs = new MenuItem(); - - Menu menu2 = new Menu(); - - MenuItem hideColumns = new MenuItem(); - - MenuItem hideSequences = new MenuItem(); - - MenuItem hideAllButSelection = new MenuItem(); - - MenuItem hideAllSelection = new MenuItem(); - - MenuItem showAllHidden = new MenuItem(); - - Menu formatMenu = new Menu(); - - Menu selectMenu = new Menu(); - - MenuItem newView = new MenuItem(); - - /** - * Attach the alignFrame panels after embedding menus, if necessary. This used - * to be called setEmbedded, but is now creates the dropdown menus in a - * platform independent manner to avoid OSX/Mac menu appendage daftness. - * - * @param reallyEmbedded - * true to attach the view to the applet area on the page rather than - * in a new window - */ - public void createAlignFrameWindow(boolean reallyEmbedded, String title) - { - if (reallyEmbedded) - { - // //// - // Explicly build the embedded menu panel for the on-page applet - // - // view cannot be closed if its actually on the page - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Remove Seperator - embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", - Font.PLAIN, 10, false); // use our own fonts. - // and actually add the components to the applet area - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - alignPanel.setSize(viewport.applet.getSize().width, - viewport.applet.getSize().height - embeddedMenu.HEIGHT - - statusBar.HEIGHT); - viewport.applet.add(alignPanel, BorderLayout.CENTER); - final AlignFrame me = this; - viewport.applet.addFocusListener(new FocusListener() - { - - @Override - public void focusLost(FocusEvent e) - { - if (me.viewport.applet.currentAlignFrame==me) { - me.viewport.applet.currentAlignFrame = null; - }} - - @Override - public void focusGained(FocusEvent e) - { - me.viewport.applet.currentAlignFrame = me; - } - }); - viewport.applet.validate(); - } - else - { - // ////// - // test and embed menu bar if necessary. - // - if (embedMenuIfNeeded(alignPanel)) - { - // adjust for status bar height too - alignPanel.setSize(getSize().width, getSize().height - - statusBar.HEIGHT); - } - add(statusBar, BorderLayout.SOUTH); - add(alignPanel, BorderLayout.CENTER); - // and register with the applet so it can pass external API calls to us - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } - } - - /** - * create a new binding between structures in an existing jmol viewer instance - * and an alignpanel with sequences that have existing PDBFile entries. Note, - * this does not open a new Jmol window, or modify the display of the - * structures in the original jmol window. Note This method doesn't work - * without an additional javascript library to exchange messages between the - * distinct applets. See http://issues.jalview.org/browse/JAL-621 - * - * @param viewer - * JmolViewer instance - * @param sequenceIds - * - sequence Ids to search for associations - */ - public SequenceStructureBinding addStructureViewInstance( - Object jmolviewer, String[] sequenceIds) - { - org.jmol.api.JmolViewer viewer = null; - try - { - viewer = (org.jmol.api.JmolViewer) jmolviewer; - } catch (ClassCastException ex) - { - System.err.println("Unsupported viewer object :" - + jmolviewer.getClass()); - } - if (viewer == null) - { - System.err.println("Can't use this object as a structure viewer:" - + jmolviewer.getClass()); - return null; - } - SequenceI[] seqs = null; - if (sequenceIds == null || sequenceIds.length == 0) - { - seqs = viewport.getAlignment().getSequencesArray(); - } - else - { - Vector sqi = new Vector(); - AlignmentI al = viewport.getAlignment(); - for (int sid = 0; sid < sequenceIds.length; sid++) - { - SequenceI sq = al.findName(sequenceIds[sid]); - if (sq != null) - { - sqi.addElement(sq); - } - } - if (sqi.size() > 0) - { - seqs = new SequenceI[sqi.size()]; - for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) - { - seqs[sid] = (SequenceI) sqi.elementAt(sid); - } - } - else - { - return null; - } - } - ExtJmol jmv = null; - // TODO: search for a jmv that involves viewer - if (jmv == null) - { // create a new viewer/jalview binding. - jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs}); - } - return jmv; - - } - - public boolean addPdbFile(String sequenceId, String pdbEntryString, - String pdbFile) - { - SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); - boolean needtoadd = false; - if (toaddpdb != null) - { - Vector pdbe = toaddpdb.getPDBId(); - PDBEntry pdbentry = null; - if (pdbe != null && pdbe.size() > 0) - { - for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) - { - pdbentry = (PDBEntry) pdbe.elementAt(pe); - if (!pdbentry.getId().equals(pdbEntryString) - && !pdbentry.getFile().equals(pdbFile)) - { - pdbentry = null; - } - else - { - continue; - } - } - } - if (pdbentry == null) - { - pdbentry = new PDBEntry(); - pdbentry.setId(pdbEntryString); - pdbentry.setFile(pdbFile); - needtoadd = true; // add this new entry to sequence. - } - // resolve data source - // TODO: this code should be a refactored to an io package - String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); - if (protocol == null) - { - return false; - } - if (needtoadd) - { - // make a note of the access mode and add - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - } - pdbentry.getProperty().put("protocol", protocol); - toaddpdb.addPDBId(pdbentry); - } - } - return true; - } - - private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) - { - if (seqs != null) - { - Vector sequences = new Vector(); - for (int i = 0; i < seqs.length; i++) - { - if (seqs[i] != null) - { - sequences.addElement(new Object[] - { seqs[i], (chains != null) ? chains[i] : null }); - } - } - seqs = new SequenceI[sequences.size()]; - chains = new String[sequences.size()]; - for (int i = 0, isize = sequences.size(); i < isize; i++) - { - Object[] oj = (Object[]) sequences.elementAt(i); - - seqs[i] = (SequenceI) oj[0]; - chains[i] = (String) oj[1]; - } - } - return new Object[] - { seqs, chains }; - - } - - public void newStructureView(JalviewLite applet, PDBEntry pdb, - SequenceI[] seqs, String[] chains, String protocol) - { - // Scrub any null sequences from the array - Object[] sqch = cleanSeqChainArrays(seqs, chains); - seqs = (SequenceI[]) sqch[0]; - chains = (String[]) sqch[1]; - if (seqs == null || seqs.length == 0) - { - System.err - .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); - } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) - { - protocol = (String) pdb.getProperty().get("protocol"); - if (protocol == null) - { - System.err.println("Couldn't work out protocol to open structure: " - + pdb.getId()); - return; - } - } - if (applet.useXtrnalSviewer) - { - // register the association(s) and quit, don't create any windows. - StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol); - return; - } - if (applet.isAlignPdbStructures() && applet.jmolAvailable) - { - // can only do alignments with Jmol - // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; - Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); - for (int i = 0, iSize = jmols.size(); i < iSize; i++) - { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); - if (tajm.ap.alignFrame == this) - { - ajm = tajm; - break; - } - } - if (ajm != null) - { - System.err - .println("Incremental adding and aligning structure to existing Jmol view not yet implemented."); - // try and add the pdb structure - // ajm.addS - ajm = null; - } - } - // otherwise, create a new window - if (applet.jmolAvailable) - { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, - protocol); - applet.lastFrameX += 40; - applet.lastFrameY += 40; - } - else - { - new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); - } - - } - - public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb, - SequenceI[][] seqs, String[][] chains, String[] protocols) - { - // TODO Auto-generated method stub - System.err.println("Aligned Structure View: Not yet implemented."); - } - - /** - * modify the current selection, providing the user has not made a selection already. - * @param sel - sequences from this alignment - * @param csel - columns to be selected on the alignment - */ - public void select(SequenceGroup sel, ColumnSelection csel) - { - alignPanel.seqPanel.selection(sel, csel, null); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + */ +package jalview.appletgui; + +import java.net.*; +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import jalview.analysis.*; +import jalview.api.SequenceStructureBinding; +import jalview.bin.JalviewLite; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; +import jalview.structure.StructureSelectionManager; + +public class AlignFrame extends EmbmenuFrame implements ActionListener, + ItemListener, KeyListener +{ + public AlignmentPanel alignPanel; + + public AlignViewport viewport; + + int DEFAULT_WIDTH = 700; + + int DEFAULT_HEIGHT = 500; + + String jalviewServletURL; + + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, + String title, boolean embedded) + { + + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } + + try + { + jbInit(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + + viewport = new AlignViewport(al, applet); + alignPanel = new AlignmentPanel(this, viewport); + + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + + annotationPanelMenuItem.setState(viewport.showAnnotation); + displayNonconservedMenuItem.setState(viewport.getShowunconserved()); + followMouseOverFlag.setState(viewport.getFollowHighlight()); + showGroupConsensus.setState(viewport.showGroupConsensus); + showGroupConservation.setState(viewport.showGroupConservation); + showConsensusHistogram.setState(viewport.showConsensusHistogram); + showSequenceLogo.setState(viewport.showSequenceLogo); + + seqLimits.setState(viewport.showJVSuffix); + + if (applet != null) + { + String param = applet.getParameter("sortBy"); + if (param != null) + { + if (param.equalsIgnoreCase("Id")) + { + sortIDMenuItem_actionPerformed(); + } + else if (param.equalsIgnoreCase("Pairwise Identity")) + { + sortPairwiseMenuItem_actionPerformed(); + } + else if (param.equalsIgnoreCase("Length")) + { + sortLengthMenuItem_actionPerformed(); + } + } + + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) + { + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); + } + } + param = applet.getParameter("centrecolumnlabels"); + if (param != null) + { + centreColumnLabelFlag.setState(true); + centreColumnLabelFlag_stateChanged(); + } + try + { + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + DEFAULT_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + DEFAULT_HEIGHT = height; + } + } catch (Exception ex) + { + } + + } + + // Some JVMS send keyevents to Top frame or lowest panel, + // Havent worked out why yet. So add to both this frame and seqCanvas for + // now + this.addKeyListener(this); + alignPanel.seqPanel.seqCanvas.addKeyListener(this); + alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); + alignPanel.annotationPanelHolder.addKeyListener(this); + alignPanel.annotationSpaceFillerHolder.addKeyListener(this); + alignPanel.alabels.addKeyListener(this); + createAlignFrameWindow(embedded, title); + alignPanel.validate(); + alignPanel.paintAlignment(true); + } + + public AlignViewport getAlignViewport() + { + return viewport; + } + + public SeqCanvas getSeqcanvas() + { + return alignPanel.seqPanel.seqCanvas; + } + + /** + * DOCUMENT ME! + * + * @param String + * DOCUMENT ME! + */ + + public void parseFeaturesFile(String file, String type) + { + Hashtable featureLinks = new Hashtable(); + boolean featuresFile = false; + try + { + featuresFile = new jalview.io.FeaturesFile(file, type) + .parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, + featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false)); + } catch (Exception ex) + { + ex.printStackTrace(); + } + + if (featuresFile) + { + if (featureLinks.size() > 0) + { + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; + } + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + if (viewport.featureSettings != null) + { + viewport.featureSettings.refreshTable(); + } + alignPanel.paintAlignment(true); + } + + } + + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode + && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt + .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt + .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + + alignPanel.alabels.cancelDrag(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown()) + { + paste(evt.isShiftDown()); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, 1); + } + else + { + moveSelectedSequences(false); + } + break; + + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, -1); + } + else + { + moveSelectedSequences(true); + } + break; + + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(-1, 0); + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(1, 0); + break; + + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; + + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + { + this.removeAllGapsMenuItem_actionPerformed(); + } + else + { + removeGappedColumnMenuItem_actionPerformed(); + } + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) + { + invertColSel_actionPerformed(); + } + else + { + invertSequenceMenuItem_actionPerformed(); + } + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(null); + } + break; + + } + alignPanel.paintAlignment(true); + } + + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel + .getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection and indicate it should be hidden. + invertColSel_actionPerformed(); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + { + viewport.showAllHiddenSeqs(); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } + } + } + + public void keyReleased(KeyEvent evt) + { + } + + public void keyTyped(KeyEvent evt) + { + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == displayNonconservedMenuItem) + { + displayNonconservedMenuItem_actionPerformed(); + } + else if (evt.getSource() == colourTextMenuItem) + { + colourTextMenuItem_actionPerformed(); + } + else if (evt.getSource() == wrapMenuItem) + { + wrapMenuItem_actionPerformed(); + } + else if (evt.getSource() == scaleAbove) + { + viewport.setScaleAboveWrapped(scaleAbove.getState()); + } + else if (evt.getSource() == scaleLeft) + { + viewport.setScaleLeftWrapped(scaleLeft.getState()); + } + else if (evt.getSource() == scaleRight) + { + viewport.setScaleRightWrapped(scaleRight.getState()); + } + else if (evt.getSource() == seqLimits) + { + seqLimits_itemStateChanged(); + } + else if (evt.getSource() == viewBoxesMenuItem) + { + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + } + else if (evt.getSource() == viewTextMenuItem) + { + viewport.setShowText(viewTextMenuItem.getState()); + } + else if (evt.getSource() == renderGapsMenuItem) + { + viewport.setRenderGaps(renderGapsMenuItem.getState()); + } + else if (evt.getSource() == annotationPanelMenuItem) + { + viewport.setShowAnnotation(annotationPanelMenuItem.getState()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + } + else if (evt.getSource() == sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if (evt.getSource() == conservationMenuItem) + { + conservationMenuItem_actionPerformed(); + } + else if (evt.getSource() == abovePIDThreshold) + { + abovePIDThreshold_actionPerformed(); + } + else if (evt.getSource() == applyToAllGroups) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + } + else if (evt.getSource() == autoCalculate) + { + viewport.autocalculateConsensus = autoCalculate.getState(); + } + else if (evt.getSource() == this.centreColumnLabelFlag) + { + centreColumnLabelFlag_stateChanged(); + } + else if (evt.getSource() == this.followMouseOverFlag) + { + mouseOverFlag_stateChanged(); + } + else if (evt.getSource() == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (evt.getSource() == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (evt.getSource() == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (evt.getSource() == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (evt.getSource() == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } + alignPanel.paintAlignment(true); + } + + private void mouseOverFlag_stateChanged() + { + viewport.followHighlight = followMouseOverFlag.getState(); + // TODO: could kick the scrollTo mechanism to reset view for current + // searchresults. + } + + private void centreColumnLabelFlag_stateChanged() + { + viewport.centreColumnLabels = centreColumnLabelFlag.getState(); + this.alignPanel.annotationPanel.repaint(); + } + + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == loadTree) + { + loadTree_actionPerformed(); + } + else if (source == loadApplication) + { + launchFullApplication(); + } + else if (source == loadAnnotations) + { + loadAnnotations(); + } + else if (source == outputAnnotations) + { + outputAnnotations(true); + } + else if (source == outputFeatures) + { + outputFeatures(true, "Jalview"); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == pasteNew) + { + pasteNew_actionPerformed(); + } + else if (source == pasteThis) + { + pasteThis_actionPerformed(); + } + else if (source == cut) + { + cut_actionPerformed(); + } + else if (source == delete) + { + delete_actionPerformed(); + } + else if (source == grpsFromSelection) + { + makeGrpsFromSelection_actionPerformed(); + } + else if (source == deleteGroups) + { + deleteGroups_actionPerformed(); + } + else if (source == selectAllSequenceMenuItem) + { + selectAllSequenceMenuItem_actionPerformed(); + } + else if (source == deselectAllSequenceMenuItem) + { + deselectAllSequenceMenuItem_actionPerformed(); + } + else if (source == invertSequenceMenuItem) + { + invertSequenceMenuItem_actionPerformed(); + } + else if (source == invertColSel) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + } + else if (source == remove2LeftMenuItem) + { + trimAlignment(true); + } + else if (source == remove2RightMenuItem) + { + trimAlignment(false); + } + else if (source == removeGappedColumnMenuItem) + { + removeGappedColumnMenuItem_actionPerformed(); + } + else if (source == removeAllGapsMenuItem) + { + removeAllGapsMenuItem_actionPerformed(); + } + else if (source == findMenuItem) + { + findMenuItem_actionPerformed(); + } + else if (source == font) + { + new FontChooser(alignPanel); + } + else if (source == newView) + { + newView(null); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == hideSequences + && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == hideAllButSelection) + { + toggleHiddenRegions(false, false); + alignPanel.paintAlignment(true); + } + else if (source == hideAllSelection) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showAllHidden) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + else if (source == showGroupConsensus) + { + showGroupConsensus_actionPerformed(); + } + else if (source == showGroupConservation) + { + showGroupConservation_actionPerformed(); + } + else if (source == showSequenceLogo) + { + showSequenceLogo_actionPerformed(); + } + else if (source == showConsensusHistogram) + { + showConsensusHistogram_actionPerformed(); + } + else if (source == applyAutoAnnotationSettings) + { + applyAutoAnnotationSettings_actionPerformed(); + } + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if (source == alProperties) + { + StringBuffer contents = new jalview.io.AlignmentProperties( + viewport.alignment).formatAsString(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + cap.setText(contents.toString()); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: " + + getTitle(), 400, 250); + } + else if (source == overviewMenuItem) + { + overviewMenuItem_actionPerformed(); + } + else if (source == noColourmenuItem) + { + changeColour(null); + } + else if (source == clustalColour) + { + abovePIDThreshold.setState(false); + changeColour(new ClustalxColourScheme( + viewport.alignment.getSequences(), + viewport.alignment.getWidth())); + } + else if (source == zappoColour) + { + changeColour(new ZappoColourScheme()); + } + else if (source == taylorColour) + { + changeColour(new TaylorColourScheme()); + } + else if (source == hydrophobicityColour) + { + changeColour(new HydrophobicColourScheme()); + } + else if (source == helixColour) + { + changeColour(new HelixColourScheme()); + } + else if (source == strandColour) + { + changeColour(new StrandColourScheme()); + } + else if (source == turnColour) + { + changeColour(new TurnColourScheme()); + } + else if (source == buriedColour) + { + changeColour(new BuriedColourScheme()); + } + else if (source == nucleotideColour) + { + changeColour(new NucleotideColourScheme()); + } + else if (source == modifyPID) + { + modifyPID_actionPerformed(); + } + else if (source == modifyConservation) + { + modifyConservation_actionPerformed(); + } + else if (source == userDefinedColour) + { + new UserDefinedColours(alignPanel, null); + } + else if (source == PIDColour) + { + changeColour(new PIDColourScheme()); + } + else if (source == BLOSUM62Colour) + { + changeColour(new Blosum62ColourScheme()); + } + else if (source == annotationColour) + { + new AnnotationColourChooser(viewport, alignPanel); + } + else if (source == sortPairwiseMenuItem) + { + sortPairwiseMenuItem_actionPerformed(); + } + else if (source == sortIDMenuItem) + { + sortIDMenuItem_actionPerformed(); + } + else if (source == sortLengthMenuItem) + { + sortLengthMenuItem_actionPerformed(); + } + else if (source == sortGroupMenuItem) + { + sortGroupMenuItem_actionPerformed(); + } + else if (source == removeRedundancyMenuItem) + { + removeRedundancyMenuItem_actionPerformed(); + } + else if (source == pairwiseAlignmentMenuItem) + { + pairwiseAlignmentMenuItem_actionPerformed(); + } + else if (source == PCAMenuItem) + { + PCAMenuItem_actionPerformed(); + } + else if (source == averageDistanceTreeMenuItem) + { + averageDistanceTreeMenuItem_actionPerformed(); + } + else if (source == neighbourTreeMenuItem) + { + neighbourTreeMenuItem_actionPerformed(); + } + else if (source == njTreeBlosumMenuItem) + { + njTreeBlosumMenuItem_actionPerformed(); + } + else if (source == avDistanceTreeBlosumMenuItem) + { + avTreeBlosumMenuItem_actionPerformed(); + } + else if (source == documentation) + { + documentation_actionPerformed(); + } + else if (source == about) + { + about_actionPerformed(); + } + + } + + public void inputText_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); + } + + protected void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Alignment output - " + e.getActionCommand(), 600, 500); + cap.setText(new AppletFormatAdapter().formatSequences( + e.getActionCommand(), viewport.getAlignment(), + viewport.showJVSuffix)); + } + + public void loadAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your features / annotations file here."); + cap.setAnnotationImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); + + } + + public String outputAnnotations(boolean displayTextbox) + { + String annotation = new AnnotationFile().printAnnotations( + viewport.showAnnotation ? viewport.alignment + .getAlignmentAnnotation() : null, viewport.alignment + .getGroups(), + ((Alignment) viewport.alignment).alignmentProperties); + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500); + cap.setText(annotation); + } + + return annotation; + } + + private Hashtable getDisplayedFeatureCols() + { + if (alignPanel.getFeatureRenderer() != null) + { + FeatureRenderer fr = alignPanel.getFeatureRenderer(); + Hashtable fcols = new Hashtable(); + Enumeration en = viewport.featuresDisplayed.keys(); + while (en.hasMoreElements()) + { + Object col = en.nextElement(); + fcols.put(col, fr.featureColours.get(col)); + } + return fcols; + } + return null; + } + + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + if (format.equalsIgnoreCase("Jalview")) + { + features = new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + getDisplayedFeatureCols()); + } + else + { + features = new FeaturesFile().printGFFFormat( + viewport.alignment.getSequencesArray(), + getDisplayedFeatureCols()); + } + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); + + cap.setText(features); + } + + return features; + } + + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open=" + + appendProtocol(viewport.applet.getParameter("file"))); + + if (viewport.applet.getParameter("features") != null) + { + url.append("&features="); + url.append(appendProtocol(viewport.applet.getParameter("features"))); + } + + if (viewport.applet.getParameter("annotations") != null) + { + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); + } + + if (viewport.applet.getParameter("jnetfile") != null) + { + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + } + + if (viewport.applet.getParameter("defaultColour") != null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("defaultColour"))); + } + + if (viewport.applet.getParameter("userDefinedColour") != null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("userDefinedColour"))); + } + if (viewport.applet.getParameter("tree") != null) + { + url.append("&tree=" + + appendProtocol(viewport.applet.getParameter("tree"))); + } + if (viewport.applet.getParameter("treeFile") != null) + { + url.append("&tree=" + + appendProtocol(viewport.applet.getParameter("treeFile"))); + } + + showURL(url.toString(), "FULL_APP"); + } + + String removeWhiteSpace(String colour) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < colour.length(); i++) + { + if (Character.isWhitespace(colour.charAt(i))) + { + sb.append("%20"); + } + else + { + sb.append(colour.charAt(i)); + } + } + + return sb.toString(); + } + + String appendProtocol(String url) + { + try + { + new URL(url); + url = URLEncoder.encode(url); + } + /* + * When we finally deprecate 1.1 compatibility, we can start to use + * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch + * (UnsupportedEncodingException ex) { System.err.println("WARNING - + * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url); + * ex.printStackTrace(); } + */ + catch (java.net.MalformedURLException ex) + { + url = viewport.applet.getCodeBase() + url; + } + return url; + } + + public void closeMenuItem_actionPerformed() + { + PaintRefresher.RemoveComponent(alignPanel); + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + + if (PaintRefresher.components.size() == 0 && viewport.applet == null) + { + System.exit(0); + } + + this.dispose(); + } + + /** + * DOCUMENT ME! + */ + void updateEditMenuBar() + { + + if (viewport.historyList.size() > 0) + { + undoMenuItem.setEnabled(true); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setLabel("Undo " + command.getDescription()); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + } + + if (viewport.redoList.size() > 0) + { + redoMenuItem.setEnabled(true); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setLabel("Redo " + command.getDescription()); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + } + } + + public void addHistoryItem(CommandI command) + { + if (command.getSize() > 0) + { + viewport.historyList.push(command); + viewport.redoList.removeAllElements(); + updateEditMenuBar(); + viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void undoMenuItem_actionPerformed() + { + if (viewport.historyList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(null); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed() + { + if (viewport.redoList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(null); + + AlignViewport originalSource = getOriginatingSource(command); + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + + AlignViewport getOriginatingSource(CommandI command) + { + AlignViewport originalSource = null; + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered + AlignmentI al = null; + if (command instanceof EditCommand) + { + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; + break; + } + } + } + } + + if (originalSource == null) + { + // The original view is closed, we must validate + // the current view against the closed view first + if (al != null) + { + PaintRefresher.validateSequences(al, viewport.alignment); + } + + originalSource = viewport; + } + + return originalSource; + } + + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + if (up) + { + for (int i = 1; i < viewport.alignment.getHeight(); i++) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.getSequences(null).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + if (sg.getSequences(null).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i - 1); + } + } + else + { + for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } + } + + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + Vector sg = new Vector(); + if (viewport.cursorMode) + { + sg.addElement(viewport.alignment + .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() != viewport.alignment + .getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); + } + + if (sg.size() < 1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.alignment.getHeight(); i++) + { + if (!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + } + + SequenceI[] seqs1 = new SequenceI[sg.size()]; + for (int i = 0; i < sg.size(); i++) + seqs1[i] = (SequenceI) sg.elementAt(i); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + seqs2[i] = (SequenceI) invertGroup.elementAt(i); + + SlideSequencesCommand ssc; + if (right) + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, + size, viewport.getGapCharacter()); + else + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, + size, viewport.getGapCharacter()); + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(size, 0); + else + groupAdjustment = size; + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(-size, 0); + else + groupAdjustment = -size; + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + boolean appendHistoryItem = false; + if (viewport.historyList != null && viewport.historyList.size() > 0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .peek()); + } + + if (!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); + } + + static StringBuffer copiedSequences; + + static Vector copiedHiddenColumns; + + protected void copy_actionPerformed() + { + if (viewport.getSelectionGroup() == null) + { + return; + } + + SequenceGroup sg = viewport.getSelectionGroup(); + copiedSequences = new StringBuffer(); + Hashtable orderedSeqs = new Hashtable(); + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.alignment.findIndex(seq); + orderedSeqs.put(index + "", seq); + } + + int index = 0, startRes, endRes; + char ch; + + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() + .size(); i++) + { + int[] region = (int[]) viewport.getColumnSelection() + .getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + { region[0] - hiddenOffset, region[1] - hiddenOffset }); + } + } + else + { + copiedHiddenColumns = null; + } + + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = null; + + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) + { + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; + + break; + } + else + { + index++; + } + } + + // FIND START RES + // Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); + + // FIND END RES + // Need to find the residue preceeding index if gap + endRes = 0; + + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap((ch))) + { + endRes++; + } + } + + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } + + copiedSequences.append(seq.getName() + + "\t" + + startRes + + "\t" + + endRes + + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); + } + + } + + protected void pasteNew_actionPerformed() + { + paste(true); + } + + protected void pasteThis_actionPerformed() + { + paste(false); + } + + void paste(boolean newAlignment) + { + try + { + + if (copiedSequences == null) + { + return; + } + + StringTokenizer st = new StringTokenizer(copiedSequences.toString()); + Vector seqs = new Vector(); + while (st.hasMoreElements()) + { + String name = st.nextToken(); + int start = Integer.parseInt(st.nextToken()); + int end = Integer.parseInt(st.nextToken()); + seqs.addElement(new Sequence(name, st.nextToken(), start, end)); + } + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); + } + + if (newAlignment) + { + String newtitle = new String("Copied sequences"); + if (getTitle().startsWith("Copied sequences")) + { + newtitle = getTitle(); + } + else + { + newtitle = newtitle.concat("- from " + getTitle()); + } + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + viewport.applet, newtitle, false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + else + { + addSequences(newSeqs); + } + + } catch (Exception ex) + { + } // could be anything being pasted in here + + } + + void addSequences(SequenceI[] seqs) + { + for (int i = 0; i < seqs.length; i++) + { + viewport.alignment.addSequence(seqs[i]); + } + + // !newAlignment + addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + seqs, 0, viewport.alignment.getWidth(), viewport.alignment)); + + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.alignment.getSequences()); + + } + + protected void cut_actionPerformed() + { + copy_actionPerformed(); + delete_actionPerformed(); + } + + protected void delete_actionPerformed() + { + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } + + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + SequenceI[] cut = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + cut[i] = (SequenceI) seqs.elementAt(i); + } + + /* + * //ADD HISTORY ITEM + */ + addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, + sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.alignment)); + + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + if (viewport.getAlignment().getHeight() < 1) + { + this.setVisible(false); + } + viewport.sendSelection(); + } + + /** + * group consensus toggled + * + */ + protected void showGroupConsensus_actionPerformed() + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /** + * group conservation toggled. + */ + protected void showGroupConservation_actionPerformed() + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed() + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed() + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed() + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void makeGrpsFromSelection_actionPerformed() + { + if (viewport.getSelectionGroup() != null) + { + SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), + viewport.alignment.getGroups()); + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + // set view properties for each group + for (int g = 0; g < gps.length; g++) + { + // gps[g].setShowunconserved(viewport.getShowUnconserved()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); + viewport.alignment.addGroup(gps[g]); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + col = col.brighter(); + for (Enumeration sq = gps[g].getSequences(null).elements(); sq + .hasMoreElements(); viewport.setSequenceColour( + (SequenceI) sq.nextElement(), col)) + ; + } + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + protected void deleteGroups_actionPerformed() + { + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + + alignPanel.paintAlignment(true); + } + + public void selectAllSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = new SequenceGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + } + sg.setEndRes(viewport.alignment.getWidth() - 1); + viewport.setSelectionGroup(sg); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void deselectAllSequenceMenuItem_actionPerformed() + { + if (viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1 = null; + alignPanel.seqPanel.keyboardNo2 = null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void invertSequenceMenuItem_actionPerformed() + { + SequenceGroup sg = viewport.getSelectionGroup(); + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void invertColSel_actionPerformed() + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + void trimAlignment(boolean trimLeft) + { + ColumnSelection colSel = viewport.getColumnSelection(); + int column; + + if (colSel.size() > 0) + { + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); + } + + statusBar.setText("Removed " + trimRegion.getSize() + " columns."); + + addHistoryItem(trimRegion); + + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) + { + viewport.alignment.deleteGroup(sg); + } + } + + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + } + + public void removeGappedColumnMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, viewport.alignment); + + addHistoryItem(removeGapCols); + + statusBar.setText("Removed " + removeGapCols.getSize() + + " empty columns."); + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + viewport.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + public void removeAllGapsMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.alignment)); + + viewport.setStartRes(seq.findIndex(startRes) - 1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + public void findMenuItem_actionPerformed() + { + new Finder(alignPanel); + } + + /** + * create a new view derived from the current view + * + * @param viewtitle + * @return frame for the new view + */ + public AlignFrame newView(String viewtitle) + { + AlignmentI newal; + if (viewport.hasHiddenRows) + { + newal = new Alignment(viewport.getAlignment().getHiddenSequences() + .getFullAlignment().getSequencesArray()); + } + else + { + newal = new Alignment(viewport.alignment.getSequencesArray()); + } + + if (viewport.alignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + { + if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + { + newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + } + } + } + + AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); + + newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); + + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); + + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + viewSize++; + } + } + + String title = new String(this.getTitle()); + if (viewtitle != null) + { + title = viewtitle + " ( " + title + ")"; + } + else + { + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + title += "(View " + viewSize + ")"; + } + + newaf.setTitle(title.toString()); + + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; + return newaf; + } + + /** + * + * @return list of feature groups on the view + */ + public String[] getFeatureGroups() + { + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + return fr.getGroups(); + } + return null; + } + + /** + * get sequence feature groups that are hidden or shown + * + * @param visible + * true is visible + * @return list + */ + public String[] getFeatureGroupsOfState(boolean visible) + { + FeatureRenderer fr = null; + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + return fr.getGroups(visible); + } + return null; + } + + /** + * Change the display state for the given feature groups + * + * @param groups + * list of group strings + * @param state + * visible or invisible + */ + public void setFeatureGroupState(String[] groups, boolean state) + { + FeatureRenderer fr = null; + this.sequenceFeatures.setState(true); + viewport.showSequenceFeatures(true); + if (alignPanel != null + && (fr = alignPanel.getFeatureRenderer()) != null) + { + fr.setGroupState(groups, state); + alignPanel.seqPanel.seqCanvas.repaint(); + if (alignPanel.overviewPanel != null) + { + alignPanel.overviewPanel.updateOverviewImage(); + } + } + } + + public void seqLimits_itemStateChanged() + { + viewport.setShowJVSuffix(seqLimits.getState()); + alignPanel.fontChanged(); + alignPanel.paintAlignment(true); + } + + protected void colourTextMenuItem_actionPerformed() + { + viewport.setColourText(colourTextMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + protected void displayNonconservedMenuItem_actionPerformed() + { + viewport.setShowunconserved(displayNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + protected void wrapMenuItem_actionPerformed() + { + viewport.setWrapAlignment(wrapMenuItem.getState()); + alignPanel.setWrapAlignment(wrapMenuItem.getState()); + scaleAbove.setEnabled(wrapMenuItem.getState()); + scaleLeft.setEnabled(wrapMenuItem.getState()); + scaleRight.setEnabled(wrapMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + public void overviewMenuItem_actionPerformed() + { + if (alignPanel.overviewPanel != null) + { + return; + } + + Frame frame = new Frame(); + OverviewPanel overview = new OverviewPanel(alignPanel); + frame.add(overview); + // +50 must allow for applet frame window + jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); + + frame.pack(); + frame.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent e) + { + alignPanel.setOverviewPanel(null); + }; + }); + + alignPanel.setOverviewPanel(overview); + + } + + void changeColour(ColourSchemeI cs) + { + int threshold = 0; + + if (cs != null) + { + if (viewport.getAbovePIDThreshold()) + { + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); + + cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + + viewport.setGlobalColourScheme(cs); + } + else + { + cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); + + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + cs.setConservation(c); + + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); + + } + else + { + cs.setConservation(null); + } + + cs.setConsensus(viewport.hconsensus); + + } + viewport.setGlobalColourScheme(cs); + + if (viewport.getColourAppliesToAllGroups()) + { + Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if (cs == null) + { + sg.cs = null; + continue; + } + if (cs instanceof ClustalxColourScheme) + { + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); + } + else + { + try + { + sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + } catch (Exception ex) + { + ex.printStackTrace(); + sg.cs = cs; + } + } + + if (viewport.getAbovePIDThreshold() + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) + { + sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 0, + sg.getWidth())); + } + else + { + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(viewport.hiddenRepSequences), 0, + viewport.alignment.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + sg.cs.setConservation(c); + } + else + { + sg.cs.setConservation(null); + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + } + } + + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sequenceColoursChanged( + alignPanel); + + alignPanel.paintAlignment(true); + } + + protected void modifyPID_actionPerformed() + { + if (viewport.getAbovePIDThreshold() + && viewport.globalColourScheme != null) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); + SliderPanel.showPIDSlider(); + } + } + + protected void modifyConservation_actionPerformed() + { + if (viewport.getConservationSelected() + && viewport.globalColourScheme != null) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.globalColourScheme, "Background"); + SliderPanel.showConservationSlider(); + } + } + + protected void conservationMenuItem_actionPerformed() + { + viewport.setConservationSelected(conservationMenuItem.getState()); + + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setState(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyConservation_actionPerformed(); + } + + public void abovePIDThreshold_actionPerformed() + { + viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); + + conservationMenuItem.setState(false); + viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyPID_actionPerformed(); + } + + public void sortPairwiseMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortIDMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortLengthMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + public void sortGroupMenuItem_actionPerformed() + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + + } + + public void removeRedundancyMenuItem_actionPerformed() + { + new RedundancyPanel(alignPanel); + } + + public void pairwiseAlignmentMenuItem_actionPerformed() + { + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) + { + Frame frame = new Frame(); + frame.add(new PairwiseAlignPanel(alignPanel)); + jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, + 500); + } + } + + public void PCAMenuItem_actionPerformed() + { + // are the sequences aligned? + if (!viewport.alignment.isAligned(false)) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.paintAlignment(true); + } + + if ((viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() < 4 && viewport + .getSelectionGroup().getSize() > 0) + || viewport.getAlignment().getHeight() < 4) + { + return; + } + + try + { + new PCAPanel(viewport); + } catch (java.lang.OutOfMemoryError ex) + { + } + + } + + public void averageDistanceTreeMenuItem_actionPerformed() + { + NewTreePanel("AV", "PID", "Average distance tree using PID"); + } + + public void neighbourTreeMenuItem_actionPerformed() + { + NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + } + + protected void njTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + } + + protected void avTreeBlosumMenuItem_actionPerformed() + { + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + } + + void NewTreePanel(String type, String pwType, String title) + { + // are the sequences aligned? + if (!viewport.alignment.isAligned(false)) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.paintAlignment(true); + + } + + if ((viewport.getSelectionGroup() != null && viewport + .getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null && viewport.alignment + .getHeight() > 1)) + { + final TreePanel tp = new TreePanel(alignPanel, type, pwType); + + addTreeMenuItem(tp, title); + + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + } + } + + void loadTree_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your Newick tree file here."); + cap.setTreeImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + } + + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); + } + + /** + * sort the alignment using the given treePanel + * + * @param treePanel + * tree used to sort view + * @param title + * string used for undo event name + */ + public void sortByTree(TreePanel treePanel, String title) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter + .sortByTree(viewport.getAlignment(), treePanel.getTree()); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); + addHistoryItem(new OrderCommand("Order by " + title, oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + /** + * Do any automatic reordering of the alignment and add the necessary bits to + * the menu structure for the new tree + * + * @param treePanel + * @param title + */ + protected void addTreeMenuItem(final TreePanel treePanel, + final String title) + { + final MenuItem item = new MenuItem(title); + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + sortByTree(treePanel, title); // treePanel.getTitle()); + } + }); + + treePanel.addWindowListener(new WindowAdapter() + { + public void windowOpened(WindowEvent e) + { + if (viewport.sortByTree) + { + sortByTree(treePanel, title); + } + super.windowOpened(e); + } + + public void windowClosing(WindowEvent e) + { + sortByTreeMenu.remove(item); + }; + }); + } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment() + .getSequencesArray(); + if (viewport.applet.debug) + { + System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'"); + } + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname!=null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment)); + } + alignPanel.paintAlignment(true); + return true; + } + protected void documentation_actionPerformed() + { + showURL("http://www.jalview.org/help.html", "HELP"); + } + + protected void about_actionPerformed() + { + + class AboutPanel extends Canvas + { + String version; + + String builddate; + + public AboutPanel(String version, String builddate) + { + this.version = version; + this.builddate = builddate; + } + + public void paint(Graphics g) + { + g.setColor(Color.white); + g.fillRect(0, 0, getSize().width, getSize().height); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + FontMetrics fm = g.getFontMetrics(); + int fh = fm.getHeight(); + int y = 5, x = 7; + g.setColor(Color.black); + // TODO: update this text for each release or centrally store it for + // lite and application + g.setFont(new Font("Helvetica", Font.BOLD, 14)); + g.drawString("JalviewLite - Release " + version, x, y += fh); + g.setFont(new Font("Helvetica", Font.BOLD, 12)); + g.drawString("Build date: " + builddate, x, y += fh); + g.setFont(new Font("Helvetica", Font.PLAIN, 12)); + g.drawString( + "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,", + x, y += fh * 1.5); + g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); + g.drawString( + "Development managed by The Barton Group, University of Dundee, Scotland, UK.", + x, y += fh); + g.drawString( + "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", + x, y += fh); + g.drawString("If you use Jalview, please cite:", x, y += fh + 8); + g.drawString( + "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)", + x, y += fh); + g.drawString( + "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench", + x, y += fh); + g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033", + x, y += fh); + } + } + + Frame frame = new Frame(); + frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite + .getBuildDate())); + jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); + + } + + public void showURL(String url, String target) + { + if (viewport.applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + if (url.indexOf(":") == -1) + { + // TODO: verify (Bas Vroling bug) prepend codebase or server URL to + // form valid URL + // Should really use docbase, not codebase. + if (url.indexOf("/") == 0) + { + String codebase = viewport.applet.getCodeBase().toString(); + url = codebase.substring(0, codebase.length() + - viewport.applet.getCodeBase().getFile().length()) + + url; + } + else + { + url = viewport.applet.getCodeBase() + url; + } + System.out.println("Show url (prepended codebase): " + url); + } + else + { + System.out.println("Show url: " + url); + } + if (url.indexOf("javascript:") == 0) + { + // no target for the javascript context + viewport.applet.getAppletContext().showDocument( + new java.net.URL(url)); + } + else + { + viewport.applet.getAppletContext().showDocument( + new java.net.URL(url), target); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + // //////////////////////////////////////////////////////////////////////////////// + // JBuilder Graphics here + + MenuBar alignFrameMenuBar = new MenuBar(); + + Menu fileMenu = new Menu("File"); + + MenuItem loadApplication = new MenuItem("View in Full Application"); + + MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + + MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + + MenuItem outputFeatures = new MenuItem("Export Features ..."); + + MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + MenuItem closeMenuItem = new MenuItem("Close"); + + Menu editMenu = new Menu("Edit"); + + Menu viewMenu = new Menu("View"); + + Menu colourMenu = new Menu("Colour"); + + Menu calculateMenu = new Menu("Calculate"); + + MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + + MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + + MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + + MenuItem remove2LeftMenuItem = new MenuItem(); + + MenuItem remove2RightMenuItem = new MenuItem(); + + MenuItem removeGappedColumnMenuItem = new MenuItem(); + + MenuItem removeAllGapsMenuItem = new MenuItem(); + + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + + MenuItem sortPairwiseMenuItem = new MenuItem(); + + MenuItem sortIDMenuItem = new MenuItem(); + + MenuItem sortLengthMenuItem = new MenuItem(); + + MenuItem sortGroupMenuItem = new MenuItem(); + + MenuItem removeRedundancyMenuItem = new MenuItem(); + + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + + MenuItem PCAMenuItem = new MenuItem(); + + MenuItem averageDistanceTreeMenuItem = new MenuItem(); + + MenuItem neighbourTreeMenuItem = new MenuItem(); + + BorderLayout borderLayout1 = new BorderLayout(); + + public Label statusBar = new Label(); + + Menu outputTextboxMenu = new Menu(); + + MenuItem clustalColour = new MenuItem(); + + MenuItem zappoColour = new MenuItem(); + + MenuItem taylorColour = new MenuItem(); + + MenuItem hydrophobicityColour = new MenuItem(); + + MenuItem helixColour = new MenuItem(); + + MenuItem strandColour = new MenuItem(); + + MenuItem turnColour = new MenuItem(); + + MenuItem buriedColour = new MenuItem(); + + MenuItem userDefinedColour = new MenuItem(); + + MenuItem PIDColour = new MenuItem(); + + MenuItem BLOSUM62Colour = new MenuItem(); + + MenuItem njTreeBlosumMenuItem = new MenuItem(); + + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + + CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); + + MenuItem alProperties = new MenuItem("Alignment Properties..."); + + MenuItem overviewMenuItem = new MenuItem(); + + MenuItem undoMenuItem = new MenuItem(); + + MenuItem redoMenuItem = new MenuItem(); + + CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + + MenuItem noColourmenuItem = new MenuItem(); + + CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + + MenuItem findMenuItem = new MenuItem(); + + CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + + MenuItem nucleotideColour = new MenuItem(); + + MenuItem deleteGroups = new MenuItem(); + + MenuItem grpsFromSelection = new MenuItem(); + + MenuItem delete = new MenuItem(); + + MenuItem copy = new MenuItem(); + + MenuItem cut = new MenuItem(); + + Menu pasteMenu = new Menu(); + + MenuItem pasteNew = new MenuItem(); + + MenuItem pasteThis = new MenuItem(); + + CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + + MenuItem font = new MenuItem(); + + CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + + CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + + CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + + MenuItem modifyPID = new MenuItem(); + + MenuItem modifyConservation = new MenuItem(); + + CheckboxMenuItem autoCalculate = new CheckboxMenuItem( + "Autocalculate Consensus", true); + + Menu sortByTreeMenu = new Menu(); + + Menu sort = new Menu(); + + Menu calculate = new Menu(); + + MenuItem inputText = new MenuItem(); + + Menu helpMenu = new Menu(); + + MenuItem documentation = new MenuItem(); + + MenuItem about = new MenuItem(); + + CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + + CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); + + CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); + Menu autoAnnMenu=new Menu(); + CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem(); + CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem(); + CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem(); + CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem(); + CheckboxMenuItem showGroupConservation = new CheckboxMenuItem(); + + private void jbInit() throws Exception + { + + setMenuBar(alignFrameMenuBar); + + MenuItem item; + + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + { + + item = new MenuItem( + jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); + + loadTree.addActionListener(this); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortLengthMenuItem.setLabel("by Length"); + sortLengthMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem + .setLabel("Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem + .setLabel("Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + displayNonconservedMenuItem.setLabel("Show nonconserved"); + displayNonconservedMenuItem.addItemListener(this); + alProperties.addActionListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + grpsFromSelection.setLabel("Make Groups for selection"); + grpsFromSelection.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + centreColumnLabelFlag.setLabel("Centre column labels"); + centreColumnLabelFlag.addItemListener(this); + followMouseOverFlag.setLabel("Automatic Scrolling"); + followMouseOverFlag.addItemListener(this); + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + featureSettings.addActionListener(this); + sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.addItemListener(this); + sequenceFeatures.setState(false); + annotationColour.setLabel("by Annotation..."); + annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)"); + hideAllSelection.setLabel("Selected Region"); + showAllHidden.setLabel("All Sequences and Columns"); + showGroupConsensus.setLabel("Group Consensus"); + showGroupConservation.setLabel("Group Conservation"); + showConsensusHistogram.setLabel("Show Consensus Histogram"); + showSequenceLogo.setLabel("Show Consensus Logo"); + applyAutoAnnotationSettings.setLabel("Apply to all groups"); + applyAutoAnnotationSettings.setState(true); + autoAnnMenu.setLabel("Autocalculated Annotation"); + + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + hideAllButSelection.addActionListener(this); + hideAllSelection.addActionListener(this); + showAllHidden.addActionListener(this); + showGroupConsensus.addItemListener(this); + showGroupConservation.addItemListener(this); + showConsensusHistogram.addItemListener(this); + showSequenceLogo.addItemListener(this); + applyAutoAnnotationSettings.addItemListener(this); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(selectMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(formatMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + + fileMenu.add(inputText); + fileMenu.add(loadTree); + fileMenu.add(loadAnnotations); + + fileMenu.addSeparator(); + fileMenu.add(outputTextboxMenu); + fileMenu.add(outputFeatures); + fileMenu.add(outputAnnotations); + + if (jalviewServletURL != null) + { + fileMenu.add(loadApplication); + } + + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); + viewMenu.add(newView); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(followMouseOverFlag); + viewMenu.add(annotationPanelMenuItem); + autoAnnMenu.add(applyAutoAnnotationSettings); + autoAnnMenu.add(showConsensusHistogram); + autoAnnMenu.add(showSequenceLogo); + autoAnnMenu.addSeparator(); + autoAnnMenu.add(showGroupConservation); + autoAnnMenu.add(showGroupConsensus); + viewMenu.add(autoAnnMenu); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(alProperties); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + colourMenu.add(annotationColour); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortLengthMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu1.add(showAllHidden); + menu2.add(hideColumns); + menu2.add(hideSequences); + menu2.add(hideAllSelection); + menu2.add(hideAllButSelection); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(displayNonconservedMenuItem); + formatMenu.add(renderGapsMenuItem); + formatMenu.add(centreColumnLabelFlag); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(grpsFromSelection); + selectMenu.add(deleteGroups); + + } + + MenuItem featureSettings = new MenuItem(); + + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + + MenuItem annotationColour = new MenuItem(); + + MenuItem invertColSel = new MenuItem(); + + Menu menu1 = new Menu(); + + MenuItem showColumns = new MenuItem(); + + MenuItem showSeqs = new MenuItem(); + + Menu menu2 = new Menu(); + + MenuItem hideColumns = new MenuItem(); + + MenuItem hideSequences = new MenuItem(); + + MenuItem hideAllButSelection = new MenuItem(); + + MenuItem hideAllSelection = new MenuItem(); + + MenuItem showAllHidden = new MenuItem(); + + Menu formatMenu = new Menu(); + + Menu selectMenu = new Menu(); + + MenuItem newView = new MenuItem(); + + /** + * Attach the alignFrame panels after embedding menus, if necessary. This used + * to be called setEmbedded, but is now creates the dropdown menus in a + * platform independent manner to avoid OSX/Mac menu appendage daftness. + * + * @param reallyEmbedded + * true to attach the view to the applet area on the page rather than + * in a new window + */ + public void createAlignFrameWindow(boolean reallyEmbedded, String title) + { + if (reallyEmbedded) + { + // //// + // Explicly build the embedded menu panel for the on-page applet + // + // view cannot be closed if its actually on the page + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Remove Seperator + embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", + Font.PLAIN, 10, false); // use our own fonts. + // and actually add the components to the applet area + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height - embeddedMenu.HEIGHT + - statusBar.HEIGHT); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + final AlignFrame me = this; + viewport.applet.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + if (me.viewport.applet.currentAlignFrame==me) { + me.viewport.applet.currentAlignFrame = null; + }} + + @Override + public void focusGained(FocusEvent e) + { + me.viewport.applet.currentAlignFrame = me; + } + }); + viewport.applet.validate(); + } + else + { + // ////// + // test and embed menu bar if necessary. + // + if (embedMenuIfNeeded(alignPanel)) + { + // adjust for status bar height too + alignPanel.setSize(getSize().width, getSize().height + - statusBar.HEIGHT); + } + add(statusBar, BorderLayout.SOUTH); + add(alignPanel, BorderLayout.CENTER); + // and register with the applet so it can pass external API calls to us + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + } + + /** + * create a new binding between structures in an existing jmol viewer instance + * and an alignpanel with sequences that have existing PDBFile entries. Note, + * this does not open a new Jmol window, or modify the display of the + * structures in the original jmol window. Note This method doesn't work + * without an additional javascript library to exchange messages between the + * distinct applets. See http://issues.jalview.org/browse/JAL-621 + * + * @param viewer + * JmolViewer instance + * @param sequenceIds + * - sequence Ids to search for associations + */ + public SequenceStructureBinding addStructureViewInstance( + Object jmolviewer, String[] sequenceIds) + { + org.jmol.api.JmolViewer viewer = null; + try + { + viewer = (org.jmol.api.JmolViewer) jmolviewer; + } catch (ClassCastException ex) + { + System.err.println("Unsupported viewer object :" + + jmolviewer.getClass()); + } + if (viewer == null) + { + System.err.println("Can't use this object as a structure viewer:" + + jmolviewer.getClass()); + return null; + } + SequenceI[] seqs = null; + if (sequenceIds == null || sequenceIds.length == 0) + { + seqs = viewport.getAlignment().getSequencesArray(); + } + else + { + Vector sqi = new Vector(); + AlignmentI al = viewport.getAlignment(); + for (int sid = 0; sid < sequenceIds.length; sid++) + { + SequenceI sq = al.findName(sequenceIds[sid]); + if (sq != null) + { + sqi.addElement(sq); + } + } + if (sqi.size() > 0) + { + seqs = new SequenceI[sqi.size()]; + for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++) + { + seqs[sid] = (SequenceI) sqi.elementAt(sid); + } + } + else + { + return null; + } + } + ExtJmol jmv = null; + // TODO: search for a jmv that involves viewer + if (jmv == null) + { // create a new viewer/jalview binding. + jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs}); + } + return jmv; + + } + /** + * bind a pdb file to a sequence in the current view + * + * @param sequenceId + * - sequenceId within the dataset. + * @param pdbEntryString + * - the short name for the PDB file + * @param pdbFile + * - pdb file - either a URL or a valid PDB file. + * @return true if binding was as success TODO: consider making an exception + * structure for indicating when PDB parsing or sequenceId location + * fails. + */ + public boolean addPdbFile(String sequenceId, String pdbEntryString, + String pdbFile) + { + SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId); + boolean needtoadd = false; + if (toaddpdb != null) + { + Vector pdbe = toaddpdb.getPDBId(); + PDBEntry pdbentry = null; + if (pdbe != null && pdbe.size() > 0) + { + for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) + { + pdbentry = (PDBEntry) pdbe.elementAt(pe); + if (!pdbentry.getId().equals(pdbEntryString) + && !pdbentry.getFile().equals(pdbFile)) + { + pdbentry = null; + } + else + { + continue; + } + } + } + if (pdbentry == null) + { + pdbentry = new PDBEntry(); + pdbentry.setId(pdbEntryString); + pdbentry.setFile(pdbFile); + needtoadd = true; // add this new entry to sequence. + } + // resolve data source + // TODO: this code should be a refactored to an io package + String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + if (protocol == null) + { + return false; + } + if (needtoadd) + { + // make a note of the access mode and add + if (pdbentry.getProperty() == null) + { + pdbentry.setProperty(new Hashtable()); + } + pdbentry.getProperty().put("protocol", protocol); + toaddpdb.addPDBId(pdbentry); + } + } + return true; + } + + private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains) + { + if (seqs != null) + { + Vector sequences = new Vector(); + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i] != null) + { + sequences.addElement(new Object[] + { seqs[i], (chains != null) ? chains[i] : null }); + } + } + seqs = new SequenceI[sequences.size()]; + chains = new String[sequences.size()]; + for (int i = 0, isize = sequences.size(); i < isize; i++) + { + Object[] oj = (Object[]) sequences.elementAt(i); + + seqs[i] = (SequenceI) oj[0]; + chains[i] = (String) oj[1]; + } + } + return new Object[] + { seqs, chains }; + + } + + public void newStructureView(JalviewLite applet, PDBEntry pdb, + SequenceI[] seqs, String[] chains, String protocol) + { + // Scrub any null sequences from the array + Object[] sqch = cleanSeqChainArrays(seqs, chains); + seqs = (SequenceI[]) sqch[0]; + chains = (String[]) sqch[1]; + if (seqs == null || seqs.length == 0) + { + System.err + .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); + } + if (protocol == null || protocol.trim().length() == 0 + || protocol.equals("null")) + { + protocol = (String) pdb.getProperty().get("protocol"); + if (protocol == null) + { + System.err.println("Couldn't work out protocol to open structure: " + + pdb.getId()); + return; + } + } + if (applet.useXtrnalSviewer) + { + // register the association(s) and quit, don't create any windows. + if (StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol)==null) { + System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences"); + } + return; + } + if (applet.isAlignPdbStructures() && applet.jmolAvailable) + { + // can only do alignments with Jmol + // find the last jmol window assigned to this alignment + jalview.appletgui.AppletJmol ajm = null, tajm; + Vector jmols = applet + .getAppletWindow(jalview.appletgui.AppletJmol.class); + for (int i = 0, iSize = jmols.size(); i < iSize; i++) + { + tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + if (tajm.ap.alignFrame == this) + { + ajm = tajm; + break; + } + } + if (ajm != null) + { + System.err + .println("Incremental adding and aligning structure to existing Jmol view not yet implemented."); + // try and add the pdb structure + // ajm.addS + ajm = null; + } + } + // otherwise, create a new window + if (applet.jmolAvailable) + { + new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + protocol); + applet.lastFrameX += 40; + applet.lastFrameY += 40; + } + else + { + new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol); + } + + } + + public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb, + SequenceI[][] seqs, String[][] chains, String[] protocols) + { + // TODO Auto-generated method stub + System.err.println("Aligned Structure View: Not yet implemented."); + } + + /** + * modify the current selection, providing the user has not made a selection already. + * @param sel - sequences from this alignment + * @param csel - columns to be selected on the alignment + */ + public void select(SequenceGroup sel, ColumnSelection csel) + { + alignPanel.seqPanel.selection(sel, csel, null); + } +} -- 1.7.10.2