X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=648b64250fa2a9703eefe75b063fe00d1ba1165f;hb=5d5387084823fabaff0069493688221c43dd93e7;hp=e17af3893d7eff39cd9be75d8741c165da771b9b;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index e17af38..648b642 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,22 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.appletgui; import java.io.*; @@ -32,21 +31,21 @@ import jalview.datamodel.*; import jalview.io.*; import jalview.schemes.*; -public class AlignFrame - extends Frame implements ActionListener, - ItemListener, KeyListener, MouseListener +public class AlignFrame extends EmbmenuFrame implements ActionListener, + ItemListener, KeyListener { public AlignmentPanel alignPanel; + public AlignViewport viewport; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; String jalviewServletURL; - public AlignFrame(AlignmentI al, - jalview.bin.JalviewLite applet, - String title, - boolean embedded) + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, + String title, boolean embedded) { if (applet != null) @@ -57,8 +56,7 @@ public class AlignFrame try { jbInit(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -70,6 +68,7 @@ public class AlignFrame viewport.updateConsensus(alignPanel); annotationPanelMenuItem.setState(viewport.showAnnotation); + displayNonconservedMenuItem.setState(viewport.getShowunconserved()); seqLimits.setState(viewport.showJVSuffix); @@ -97,7 +96,12 @@ public class AlignFrame wrapMenuItem_actionPerformed(); } } - + param = applet.getParameter("centrecolumnlabels"); + if (param != null) + { + centreColumnLabelFlag.setState(true); + centreColumnLabelFlag_stateChanged(); + } try { param = applet.getParameter("windowWidth"); @@ -112,30 +116,21 @@ public class AlignFrame int height = Integer.parseInt(param); DEFAULT_HEIGHT = height; } + } catch (Exception ex) + { } - catch (Exception ex) - {} } - //Some JVMS send keyevents to Top frame or lowest panel, - //Havent worked out why yet. So add to both this frame and seqCanvas for now + // Some JVMS send keyevents to Top frame or lowest panel, + // Havent worked out why yet. So add to both this frame and seqCanvas for + // now this.addKeyListener(this); alignPanel.seqPanel.seqCanvas.addKeyListener(this); alignPanel.idPanel.idCanvas.addKeyListener(this); alignPanel.scalePanel.addKeyListener(this); alignPanel.annotationPanel.addKeyListener(this); - - if (embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } + createAlignFrameWindow(embedded, title); alignPanel.validate(); alignPanel.paintAlignment(true); } @@ -152,8 +147,9 @@ public class AlignFrame /** * DOCUMENT ME! - * - * @param String DOCUMENT ME! + * + * @param String + * DOCUMENT ME! */ public void parseFeaturesFile(String file, String type) @@ -162,14 +158,11 @@ public class AlignFrame boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, - type).parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas. - getFeatureRenderer().featureColours, - featureLinks, - true); - } - catch (Exception ex) + featuresFile = new jalview.io.FeaturesFile(file, type).parse( + viewport.alignment, alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, featureLinks, + true); + } catch (Exception ex) { ex.printStackTrace(); } @@ -178,8 +171,7 @@ public class AlignFrame { if (featureLinks.size() > 0) { - alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureLinks = featureLinks; + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; } viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); @@ -190,311 +182,306 @@ public class AlignFrame public void keyPressed(KeyEvent evt) { - if (viewport.cursorMode && - ( (evt.getKeyCode() >= KeyEvent.VK_0 && - evt.getKeyCode() <= KeyEvent.VK_9) - || - (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && - evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) - ) - && Character.isDigit(evt.getKeyChar())) - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); - + if (viewport.cursorMode + && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt + .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt + .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); switch (evt.getKeyCode()) { - case 27: // escape key - deselectAllSequenceMenuItem_actionPerformed(); - break; - case KeyEvent.VK_X: - if (evt.isControlDown() || evt.isMetaDown()) - { - cut_actionPerformed(); - } - break; - case KeyEvent.VK_C: - if (viewport.cursorMode && !evt.isControlDown()) - { - alignPanel.seqPanel.setCursorColumn(); - } - if (evt.isControlDown() || evt.isMetaDown()) - { - copy_actionPerformed(); - } - break; - case KeyEvent.VK_V: - if (evt.isControlDown()) - { - paste(evt.isShiftDown()); - } - break; - case KeyEvent.VK_A: - if (evt.isControlDown() || evt.isMetaDown()) - { - selectAllSequenceMenuItem_actionPerformed(); - } - break; - case KeyEvent.VK_DOWN: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0, 1); - } - else - { - moveSelectedSequences(false); - } - break; + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + if (evt.isControlDown() || evt.isMetaDown()) + { + copy_actionPerformed(); + } + break; + case KeyEvent.VK_V: + if (evt.isControlDown()) + { + paste(evt.isShiftDown()); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, 1); + } + else + { + moveSelectedSequences(false); + } + break; - case KeyEvent.VK_UP: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(0, -1); - } - else - { - moveSelectedSequences(true); - } - break; + case KeyEvent.VK_UP: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0, -1); + } + else + { + moveSelectedSequences(true); + } + break; - case KeyEvent.VK_LEFT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(false, - alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor( -1, 0); - break; + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(-1, 0); + break; - case KeyEvent.VK_RIGHT: - if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, - alignPanel.seqPanel.getKeyboardNo1()); - else - alignPanel.seqPanel.moveCursor( 1, 0); - break; + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(1, 0); + break; - case KeyEvent.VK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() - || evt.isShiftDown() - || evt.isAltDown() - ); - } - break; + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + break; - case KeyEvent.VK_DELETE: - case KeyEvent.VK_BACK_SPACE: - if (viewport.cursorMode) - { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() - || evt.isShiftDown() - || evt.isAltDown()); - } - else - { - cut_actionPerformed(); - alignPanel.seqPanel.seqCanvas.repaint(); - } - break; + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; - case KeyEvent.VK_S: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRow(); - } - break; - case KeyEvent.VK_P: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorPosition(); - } - break; + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; - case KeyEvent.VK_ENTER: - case KeyEvent.VK_COMMA: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setCursorRowAndColumn(); - } - break; + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; - case KeyEvent.VK_Q: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); - } - break; - case KeyEvent.VK_M: - if (viewport.cursorMode) - { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); - } - break; + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; - case KeyEvent.VK_F2: - viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " + - (viewport.cursorMode ? "on" : "off")); - if (viewport.cursorMode) + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + hide = true; + viewport.hideAllSelectedSeqs(); } - break; - - case KeyEvent.VK_F: - if (evt.isControlDown()) + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) { - findMenuItem_actionPerformed(); + viewport.showAllHiddenSeqs(); } - break; + } - case KeyEvent.VK_H: + if (toggleCols) { - boolean toggleSeqs = !evt.isControlDown(); - boolean toggleCols = !evt.isShiftDown(); - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - - if (toggleSeqs) + if (viewport.colSel.getSelected().size() > 0) { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) - { - hide = true; - viewport.hideAllSelectedSeqs(); - } - else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) + viewport.hideSelectedColumns(); + if (!toggleSeqs) { - viewport.showAllHiddenSeqs(); + viewport.selectionGroup = sg; } } - - if (toggleCols) + else if (!hide) { - if (viewport.colSel.getSelected().size() > 0) - { - viewport.hideSelectedColumns(); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - viewport.showAllHiddenColumns(); - } + viewport.showAllHiddenColumns(); } - break; } + break; + } - case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(true); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - - viewport.endSeq + viewport.startSeq); - } - break; + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; - case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) - { - alignPanel.scrollUp(false); - } - else - { - alignPanel.setScrollValues(viewport.startRes, - viewport.startSeq - + viewport.endSeq - viewport.startSeq); - } - break; + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; - case KeyEvent.VK_Z: - if (evt.isControlDown()) - { - undoMenuItem_actionPerformed(); - } - break; + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; - case KeyEvent.VK_Y: - if (evt.isControlDown()) - { - redoMenuItem_actionPerformed(); - } - break; + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; - case KeyEvent.VK_L: - if (evt.isControlDown()) - { - trimAlignment(true); - } - break; + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; - case KeyEvent.VK_R: - if (evt.isControlDown()) - { - trimAlignment(false); - } - break; + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; - case KeyEvent.VK_E: - if (evt.isControlDown()) + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) { - if (evt.isShiftDown()) - { - this.removeAllGapsMenuItem_actionPerformed(); - } - else - { - removeGappedColumnMenuItem_actionPerformed(); - } + this.removeAllGapsMenuItem_actionPerformed(); } - break; - case KeyEvent.VK_I: - if (evt.isControlDown()) + else { - if (evt.isAltDown()) - { - viewport.invertColumnSelection(); - } - else - { - this.invertSequenceMenuItem_actionPerformed(); - } + removeGappedColumnMenuItem_actionPerformed(); } - break; - - case KeyEvent.VK_U: - if (evt.isControlDown()) + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) { - this.deleteGroups_actionPerformed(); + viewport.invertColumnSelection(); } - break; - - case KeyEvent.VK_T: - if (evt.isControlDown()) + else { - newView(); + this.invertSequenceMenuItem_actionPerformed(); } - break; + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(null); + } + break; } alignPanel.paintAlignment(true); } public void keyReleased(KeyEvent evt) - {} + { + } public void keyTyped(KeyEvent evt) - {} + { + } public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == colourTextMenuItem) + if (evt.getSource() == displayNonconservedMenuItem) + { + displayNonconservedMenuItem_actionPerformed(); + } + else if (evt.getSource() == colourTextMenuItem) { colourTextMenuItem_actionPerformed(); } @@ -556,10 +543,29 @@ public class AlignFrame { viewport.autocalculateConsensus = autoCalculate.getState(); } + else if (evt.getSource() == this.centreColumnLabelFlag) + { + centreColumnLabelFlag_stateChanged(); + } else if (evt.getSource() == this.followMouseOverFlag) + { + mouseOverFlag_stateChanged(); + } alignPanel.paintAlignment(true); } + private void mouseOverFlag_stateChanged() + { + viewport.followHighlight = followMouseOverFlag.getState(); + // TODO: could kick the scrollTo mechanism to reset view for current searchresults. + } + + private void centreColumnLabelFlag_stateChanged() + { + viewport.centreColumnLabels = centreColumnLabelFlag.getState(); + this.alignPanel.annotationPanel.repaint(); + } + public void actionPerformed(ActionEvent evt) { Object source = evt.getSource(); @@ -687,7 +693,7 @@ public class AlignFrame } else if (source == newView) { - newView(); + newView(null); } else if (source == showColumns) { @@ -703,7 +709,8 @@ public class AlignFrame viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } - else if (source == hideSequences && viewport.getSelectionGroup() != null) + else if (source == hideSequences + && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); } @@ -711,47 +718,46 @@ public class AlignFrame { new FeatureSettings(alignPanel); } - else if(source== alProperties) + else if (source == alProperties) { - StringBuffer contents = new StringBuffer(); + StringBuffer contents = new StringBuffer(); - float avg = 0; - int min=Integer.MAX_VALUE, max=0; - for(int i=0; imax) - max = size; - if(size max) + max = size; + if (size < min) + min = size; + } + avg = avg / (float) viewport.alignment.getHeight(); - contents.append("\nSequences: "+ viewport.alignment.getHeight()); - contents.append("\nMinimum Sequence Length: "+min); - contents.append("\nMaximum Sequence Length: "+max); - contents.append("\nAverage Length: "+(int)avg); + contents.append("\nSequences: " + viewport.alignment.getHeight()); + contents.append("\nMinimum Sequence Length: " + min); + contents.append("\nMaximum Sequence Length: " + max); + contents.append("\nAverage Length: " + (int) avg); - if (((Alignment)viewport.alignment).alignmentProperties != null) + if (((Alignment) viewport.alignment).alignmentProperties != null) + { + Hashtable props = ((Alignment) viewport.alignment).alignmentProperties; + Enumeration en = props.keys(); + while (en.hasMoreElements()) { - Hashtable props = ((Alignment)viewport.alignment).alignmentProperties; - Enumeration en = props.keys(); - while(en.hasMoreElements()) - { - String key = en.nextElement().toString(); - contents.append("\n"+key+"\t"+props.get(key)); - } + String key = en.nextElement().toString(); + contents.append("\n" + key + "\t" + props.get(key)); } + } - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); - cap.setText(contents.toString()); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment Properties: "+getTitle() - , 400, 250); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + cap.setText(contents.toString()); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: " + + getTitle(), 400, 250); } else if (source == overviewMenuItem) { @@ -764,8 +770,8 @@ public class AlignFrame else if (source == clustalColour) { abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), - viewport.alignment.getWidth())); + changeColour(new ClustalxColourScheme(viewport.alignment + .getSequences(), viewport.alignment.getWidth())); } else if (source == zappoColour) { @@ -887,12 +893,11 @@ public class AlignFrame CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Alignment output - " + e.getActionCommand(), - 600, 500); - cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment(), - viewport.showJVSuffix)); + jalview.bin.JalviewLite.addFrame(frame, "Alignment output - " + + e.getActionCommand(), 600, 500); + cap.setText(new AppletFormatAdapter().formatSequences(e + .getActionCommand(), viewport.getAlignment(), + viewport.showJVSuffix)); } public void loadAnnotations() @@ -909,18 +914,17 @@ public class AlignFrame public String outputAnnotations(boolean displayTextbox) { String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, - viewport.alignment.getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + viewport.showAnnotation ? viewport.alignment + .getAlignmentAnnotation() : null, viewport.alignment + .getGroups(), + ((Alignment) viewport.alignment).alignmentProperties); if (displayTextbox) { CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Annotations", - 600, 500); + jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500); cap.setText(annotation); } @@ -932,15 +936,13 @@ public class AlignFrame String features; if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat( - viewport.alignment.getSequencesArray(), - viewport.featuresDisplayed); + features = new FeaturesFile().printJalviewFormat(viewport.alignment + .getSequencesArray(), viewport.featuresDisplayed); } else { - features = new FeaturesFile().printGFFFormat( - viewport.alignment.getSequencesArray(), - viewport.featuresDisplayed); + features = new FeaturesFile().printGFFFormat(viewport.alignment + .getSequencesArray(), viewport.featuresDisplayed); } if (displayTextbox) @@ -948,9 +950,7 @@ public class AlignFrame CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, - "Features", - 600, 500); + jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500); cap.setText(features); } @@ -962,8 +962,8 @@ public class AlignFrame { StringBuffer url = new StringBuffer(jalviewServletURL); - url.append("?open=" + - appendProtocol(viewport.applet.getParameter("file"))); + url.append("?open=" + + appendProtocol(viewport.applet.getParameter("file"))); if (viewport.applet.getParameter("features") != null) { @@ -974,7 +974,9 @@ public class AlignFrame if (viewport.applet.getParameter("annotations") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("annotations"))); + url + .append(appendProtocol(viewport.applet + .getParameter("annotations"))); } if (viewport.applet.getParameter("jnetfile") != null) @@ -985,17 +987,26 @@ public class AlignFrame if (viewport.applet.getParameter("defaultColour") != null) { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter("defaultColour")) - ); + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("defaultColour"))); } if (viewport.applet.getParameter("userDefinedColour") != null) { - url.append("&colour=" + - removeWhiteSpace(viewport.applet.getParameter( - "userDefinedColour")) - ); + url.append("&colour=" + + removeWhiteSpace(viewport.applet + .getParameter("userDefinedColour"))); + } + if (viewport.applet.getParameter("tree") != null) + { + 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"); @@ -1024,7 +1035,15 @@ public class AlignFrame 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; @@ -1088,10 +1107,12 @@ public class AlignFrame viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; } } + /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed() { @@ -1109,13 +1130,14 @@ public class AlignFrame originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; updateEditMenuBar(); originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.alignment.getSequences()); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed() { @@ -1133,29 +1155,29 @@ public class AlignFrame updateEditMenuBar(); originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + originalSource.alignment.getSequences()); } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; - //For sequence removal and addition, we need to fire - //the property change event FROM the viewport where the - //original alignment was altered + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - Vector comps = (Vector) PaintRefresher.components - .get(viewport.getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) { - originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; } } @@ -1164,8 +1186,8 @@ public class AlignFrame if (originalSource == null) { - //The original view is closed, we must validate - //the current view against the closed view first + // The original view is closed, we must validate + // the current view against the closed view first if (al != null) { PaintRefresher.validateSequences(al, viewport.alignment); @@ -1232,19 +1254,20 @@ public class AlignFrame synchronized void slideSequences(boolean right, int size) { Vector sg = new Vector(); - if(viewport.cursorMode) + if (viewport.cursorMode) { - sg.addElement(viewport.alignment.getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + 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); } - else if(viewport.getSelectionGroup()!=null - && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) - { - sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); - } - if(sg.size()<1) + if (sg.size() < 1) { return; } @@ -1253,8 +1276,8 @@ public class AlignFrame for (int i = 0; i < viewport.alignment.getHeight(); i++) { - if(!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.addElement(viewport.alignment.getSequenceAt(i)); } SequenceI[] seqs1 = new SequenceI[sg.size()]; @@ -1267,15 +1290,11 @@ public class AlignFrame SlideSequencesCommand ssc; if (right) - ssc = new SlideSequencesCommand("Slide Sequences", - seqs2, seqs1, size, - viewport.getGapCharacter() - ); + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, + size, viewport.getGapCharacter()); else - ssc = new SlideSequencesCommand("Slide Sequences", - seqs1, seqs2, size, - viewport.getGapCharacter() - ); + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, + size, viewport.getGapCharacter()); int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) @@ -1288,7 +1307,7 @@ public class AlignFrame else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor( -size, 0); + alignPanel.seqPanel.moveCursor(-size, 0); else groupAdjustment = -size; } @@ -1296,30 +1315,30 @@ public class AlignFrame if (groupAdjustment != 0) { viewport.getSelectionGroup().setStartRes( - viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().getStartRes() + groupAdjustment); viewport.getSelectionGroup().setEndRes( - viewport.getSelectionGroup().getEndRes() + groupAdjustment); + viewport.getSelectionGroup().getEndRes() + groupAdjustment); } - boolean appendHistoryItem = false; - if(viewport.historyList!=null - && viewport.historyList.size()>0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + if (viewport.historyList != null && viewport.historyList.size() > 0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) { - appendHistoryItem = ssc.appendSlideCommand( - (SlideSequencesCommand)viewport.historyList.peek()) - ; + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .peek()); } - if(!appendHistoryItem) + if (!appendHistoryItem) addHistoryItem(ssc); repaint(); } static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -1344,15 +1363,14 @@ public class AlignFrame { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); - i++) + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() + .size(); i++) { - int[] region = (int[]) - viewport.getColumnSelection().getHiddenColumns().elementAt(i); + int[] region = (int[]) viewport.getColumnSelection() + .getHiddenColumns().elementAt(i); copiedHiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1] - hiddenOffset}); + { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } else @@ -1379,18 +1397,18 @@ public class AlignFrame } } - //FIND START RES - //Returns residue following index if gap + // FIND START RES + // Returns residue following index if gap startRes = seq.findPosition(sg.getStartRes()); - //FIND END RES - //Need to find the residue preceeding index if gap + // FIND END RES + // Need to find the residue preceeding index if gap endRes = 0; for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) { ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) + if (!jalview.util.Comparison.isGap((ch))) { endRes++; } @@ -1401,11 +1419,14 @@ public class AlignFrame endRes += seq.getStart() - 1; } - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + + "\t" + + startRes + + "\t" + + endRes + + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); } } @@ -1457,9 +1478,7 @@ public class AlignFrame newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), - viewport.applet, - newtitle, - false); + viewport.applet, newtitle, false); if (copiedHiddenColumns != null) { for (int i = 0; i < copiedHiddenColumns.size(); i++) @@ -1470,16 +1489,16 @@ public class AlignFrame } jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + DEFAULT_HEIGHT); } else { addSequences(newSeqs); } - } - catch (Exception ex) - {} // could be anything being pasted in here + } catch (Exception ex) + { + } // could be anything being pasted in here } @@ -1490,20 +1509,14 @@ public class AlignFrame viewport.alignment.addSequence(seqs[i]); } - //!newAlignment - addHistoryItem(new EditCommand( - "Add sequences", - EditCommand.PASTE, - seqs, - 0, - viewport.alignment.getWidth(), - viewport.alignment) - ); + // !newAlignment + addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + seqs, 0, viewport.alignment.getWidth(), viewport.alignment)); viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, - viewport.alignment.getSequences()); + viewport.firePropertyChange("alignment", null, viewport.alignment + .getSequences()); } @@ -1534,7 +1547,7 @@ public class AlignFrame if (sg.getSize() == viewport.alignment.getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); + sg.getEndRes() + 1); } SequenceI[] cut = new SequenceI[seqs.size()]; @@ -1544,20 +1557,17 @@ public class AlignFrame } /* - //ADD HISTORY ITEM + * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", - EditCommand.CUT, - cut, - sg.getStartRes(), - sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, + sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.alignment)); viewport.setSelectionGroup(null); viewport.alignment.deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); if (viewport.getAlignment().getHeight() < 1) { @@ -1633,8 +1643,8 @@ public class AlignFrame SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); } else { @@ -1645,23 +1655,17 @@ public class AlignFrame if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_LEFT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_RIGHT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); } statusBar.setText("Removed " + trimRegion.getSize() + " columns."); @@ -1674,15 +1678,15 @@ public class AlignFrame { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if ( (trimLeft && !sg.adjustForRemoveLeft(column)) - || (!trimLeft && !sg.adjustForRemoveRight(column))) + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); } } @@ -1693,8 +1697,8 @@ public class AlignFrame SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1703,28 +1707,26 @@ public class AlignFrame seqs = viewport.alignment.getSequencesArray(); } - RemoveGapColCommand removeGapCols = - new RemoveGapColCommand("Remove Gapped Columns", - seqs, - start, end, - viewport.alignment); + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, viewport.alignment); addHistoryItem(removeGapCols); - statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns."); + statusBar.setText("Removed " + removeGapCols.getSize() + + " empty columns."); - //This is to maintain viewport position on first residue - //of first sequence + // This is to maintain viewport position on first residue + // of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) - // viewport.getColumnSelection().compensateForEdits(shifts); + // viewport.getColumnSelection().compensateForEdits(shifts); viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } @@ -1735,8 +1737,8 @@ public class AlignFrame SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. - hiddenRepSequences); + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -1745,20 +1747,18 @@ public class AlignFrame seqs = viewport.alignment.getSequencesArray(); } - //This is to maintain viewport position on first residue - //of first sequence + // This is to maintain viewport position on first residue + // of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); - addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.alignment)); + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.alignment)); viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); } @@ -1767,15 +1767,19 @@ public class AlignFrame new Finder(alignPanel); } - public void newView() + /** + * 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()); + newal = new Alignment(viewport.getAlignment().getHiddenSequences() + .getFullAlignment().getSequencesArray()); } else { @@ -1788,28 +1792,27 @@ public class AlignFrame { if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) { - newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + newal + .addAnnotation(viewport.alignment + .getAlignmentAnnotation()[i]); } } } - AlignFrame newaf = new AlignFrame(newal, - viewport.applet, - "", - false); + AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false); newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); - PaintRefresher.Register(newaf.alignPanel, - newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, newaf.alignPanel.av + .getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, - newaf.alignPanel.av.getSequenceSetId()); + newaf.alignPanel.av.getSequenceSetId()); PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, - newaf.alignPanel.av.getSequenceSetId()); + newaf.alignPanel.av.getSequenceSetId()); - Vector comps = (Vector) PaintRefresher.components.get(viewport. - getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); int viewSize = -1; for (int i = 0; i < comps.size(); i++) { @@ -1820,18 +1823,82 @@ public class AlignFrame } String title = new String(this.getTitle()); - if (title.indexOf("(View") > -1) + if (viewtitle != null) { - title = title.substring(0, title.indexOf("(View")); + title = viewtitle + " ( " + title + ")"; + } + else + { + if (title.indexOf("(View") > -1) + { + title = title.substring(0, title.indexOf("(View")); + } + title += "(View " + viewSize + ")"; } - - 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() @@ -1847,6 +1914,12 @@ public class AlignFrame alignPanel.paintAlignment(true); } + protected void displayNonconservedMenuItem_actionPerformed() + { + viewport.setShowunconserved(displayNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + protected void wrapMenuItem_actionPerformed() { viewport.setWrapAlignment(wrapMenuItem.getState()); @@ -1869,8 +1942,8 @@ public class AlignFrame frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.getPreferredSize().width, - overview.getPreferredSize().height + 50); + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); frame.pack(); frame.addWindowListener(new WindowAdapter() @@ -1893,7 +1966,8 @@ public class AlignFrame { if (viewport.getAbovePIDThreshold()) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background"); + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); @@ -1909,17 +1983,16 @@ public class AlignFrame Alignment al = (Alignment) viewport.alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, al + .getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); cs.setConservation(c); - cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, - "Background")); + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); } else @@ -1946,17 +2019,15 @@ public class AlignFrame } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme( - sg.getSequences(viewport.hiddenRepSequences), - sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg + .getSequences(viewport.hiddenRepSequences), sg.getWidth()); } else { try { sg.cs = (ColourSchemeI) cs.getClass().newInstance(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); sg.cs = cs; @@ -1964,12 +2035,13 @@ public class AlignFrame } if (viewport.getAbovePIDThreshold() - || cs instanceof PIDColourScheme - || cs instanceof Blosum62ColourScheme) + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg + .getSequences(viewport.hiddenRepSequences), 0, sg + .getWidth())); } else { @@ -1979,10 +2051,9 @@ public class AlignFrame if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(viewport. - hiddenRepSequences), 0, - viewport.alignment.getWidth() - 1); + ResidueProperties.propHash, 3, sg + .getSequences(viewport.hiddenRepSequences), 0, + viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); sg.cs.setConservation(c); @@ -2001,28 +2072,31 @@ public class AlignFrame alignPanel.getOverviewPanel().updateOverviewImage(); } - jalview.structure.StructureSelectionManager.getStructureSelectionManager() - .sequenceColoursChanged(alignPanel); + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sequenceColoursChanged( + alignPanel); alignPanel.paintAlignment(true); } protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) + if (viewport.getAbovePIDThreshold() + && viewport.globalColourScheme != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(alignPanel, viewport + .getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() && viewport.globalColourScheme != null) + if (viewport.getConservationSelected() + && viewport.globalColourScheme != null) { - SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, - "Background"); + SliderPanel.setConservationSlider(alignPanel, + viewport.globalColourScheme, "Background"); SliderPanel.showConservationSlider(); } } @@ -2050,30 +2124,32 @@ public class AlignFrame modifyPID_actionPerformed(); } - public void sortPairwiseMenuItem_actionPerformed() { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), - viewport.getAlignment().getSequenceAt(0)); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.alignment)); alignPanel.paintAlignment(true); } public void sortIDMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - // HistoryItem.SORT)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } public void sortGroupMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - // HistoryItem.SORT)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } @@ -2086,24 +2162,24 @@ public class AlignFrame public void pairwiseAlignmentMenuItem_actionPerformed() { if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() > 1) + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); + jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, + 500); } } public void PCAMenuItem_actionPerformed() { - //are the sequences aligned? + // are the sequences aligned? if (!viewport.alignment.isAligned()) { SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -2115,10 +2191,10 @@ public class AlignFrame alignPanel.paintAlignment(true); } - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) - || viewport.getAlignment().getHeight() < 4) + if ((viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() < 4 && viewport + .getSelectionGroup().getSize() > 0) + || viewport.getAlignment().getHeight() < 4) { return; } @@ -2126,8 +2202,7 @@ public class AlignFrame try { new PCAPanel(viewport); - } - catch (java.lang.OutOfMemoryError ex) + } catch (java.lang.OutOfMemoryError ex) { } @@ -2155,14 +2230,13 @@ public class AlignFrame void NewTreePanel(String type, String pwType, String title) { - //are the sequences aligned? + // are the sequences aligned? if (!viewport.alignment.isAligned()) { SequenceI current; int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) { current = viewport.getAlignment().getSequenceAt(i); @@ -2175,14 +2249,12 @@ public class AlignFrame } - if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 1) - || (viewport.getSelectionGroup() == null - && viewport.alignment.getHeight() > 1)) + if ((viewport.getSelectionGroup() != null && viewport + .getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null && viewport.alignment + .getHeight() > 1)) { - final TreePanel tp = new TreePanel(viewport, - type, - pwType); + final TreePanel tp = new TreePanel(viewport, type, pwType); addTreeMenuItem(tp, title); @@ -2202,15 +2274,32 @@ public class AlignFrame public void loadTree(jalview.io.NewickFile tree, String treeFile) { - TreePanel tp = new TreePanel(viewport, - treeFile, - "From File - ", - tree); + TreePanel tp = new TreePanel(viewport, treeFile, "From File - ", tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } - - void addTreeMenuItem(final TreePanel treePanel, String title) + /** + * sort the alignment using the given treePanel + * @param treePanel tree used to sort view + * @param title string used for undo event name + */ + public void sortByTree(TreePanel treePanel, String title) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel + .getTree()); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); + addHistoryItem(new OrderCommand("Order by "+title, oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + /** + * Do any automatic reordering of the alignment and add the necessary bits to the menu structure for the new tree + * @param treePanel + * @param title + */ + protected void addTreeMenuItem(final TreePanel treePanel, final String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); @@ -2218,15 +2307,21 @@ public class AlignFrame { public void actionPerformed(ActionEvent evt) { - // addHistoryItem(new HistoryItem("Sort", viewport.alignment, - // HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.paintAlignment(true); + sortByTree(treePanel, title); // treePanel.getTitle()); } }); treePanel.addWindowListener(new WindowAdapter() { + public void windowOpened(WindowEvent e) + { + if (viewport.sortByTree) + { + sortByTree(treePanel, title); + } + super.windowOpened(e); + } + public void windowClosing(WindowEvent e) { sortByTreeMenu.remove(item); @@ -2242,10 +2337,10 @@ public class AlignFrame protected void about_actionPerformed() { - class AboutPanel - extends Canvas + class AboutPanel extends Canvas { String version; + public AboutPanel(String version) { this.version = version; @@ -2260,20 +2355,29 @@ public class AlignFrame int fh = fm.getHeight(); int y = 5, x = 7; g.setColor(Color.black); + // TODO: update this text for each release or centrally store it for + // lite and application g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release " + version, 200, y += fh); + g.drawString("JalviewLite - Release " + version, x, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); - g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", - x, y += fh * 2); - g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.", - x, y += fh); + g + .drawString( + "Authors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,", + x, y += fh * 1.5); + g.drawString("David Martin & Geoff Barton.", x + 50, y += fh); + g + .drawString( + "Development managed by The Barton Group, University of Dundee, Scotland, UK.", + x, y += fh); + g + .drawString( + "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list", + x, y += fh); + g.drawString("If you use Jalview, please cite:", x, y += fh + 8); g.drawString( - "For any issues relating to Jalview, email help@jalview.org", x, - y += fh); - g.drawString("If you use JalView, please cite:", x, y += fh + 8); - g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", - x, y += fh); - g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); + "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); } } @@ -2284,17 +2388,16 @@ public class AlignFrame try { BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); + url.openStream())); String line; - while ( (line = reader.readLine()) != null) + while ((line = reader.readLine()) != null) { if (line.indexOf("VERSION") > -1) { version = line.substring(line.indexOf("=") + 1); } } - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -2302,7 +2405,7 @@ public class AlignFrame Frame frame = new Frame(); frame.add(new AboutPanel(version)); - jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); + jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220); } @@ -2316,117 +2419,202 @@ public class AlignFrame { try { - System.out.println("Show url: " + url); - viewport.applet.getAppletContext().showDocument(new java.net.URL(url), - target); - } - catch (Exception ex) + if (url.indexOf(":")==-1) + { + // TODO: verify (Bas Vroling bug) prepend codebase or server URL to form valid URL + if (url.indexOf("/")==0) + { + String codebase = viewport.applet.getCodeBase().toString(); + url = codebase.substring(0,codebase.length()-viewport.applet.getCodeBase().getFile().length())+url; + } else { + url = viewport.applet.getCodeBase()+url; + } + System.out.println("Show url (prepended codebase): " + url); + } else { + System.out.println("Show url: " + url); + } + viewport.applet.getAppletContext().showDocument( + new java.net.URL(url), target); + } catch (Exception ex) { ex.printStackTrace(); } } } - ////////////////////////////////////////////////////////////////////////////////// - //JBuilder Graphics here - - MenuBar alignFrameMenuBar = new MenuBar(); - Menu fileMenu = new Menu("File"); - MenuItem loadApplication = new MenuItem("View in Full Application"); - MenuItem loadTree = new MenuItem("Load Associated Tree ..."); - MenuItem loadAnnotations = new MenuItem( - "Load Features/Annotations ..."); - MenuItem outputFeatures = new MenuItem("Export Features ..."); - MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); - - MenuItem closeMenuItem = new MenuItem("Close"); - Menu editMenu = new Menu("Edit"); - Menu viewMenu = new Menu("View"); - Menu colourMenu = new Menu("Colour"); - Menu calculateMenu = new Menu("Calculate"); - MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - MenuItem remove2LeftMenuItem = new MenuItem(); - MenuItem remove2RightMenuItem = new MenuItem(); - MenuItem removeGappedColumnMenuItem = new MenuItem(); - MenuItem removeAllGapsMenuItem = new MenuItem(); - CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - MenuItem sortPairwiseMenuItem = new MenuItem(); - MenuItem sortIDMenuItem = new MenuItem(); - MenuItem sortGroupMenuItem = new MenuItem(); - MenuItem removeRedundancyMenuItem = new MenuItem(); - MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - MenuItem PCAMenuItem = new MenuItem(); - MenuItem averageDistanceTreeMenuItem = new MenuItem(); - MenuItem neighbourTreeMenuItem = new MenuItem(); + // //////////////////////////////////////////////////////////////////////////////// + // JBuilder Graphics here + + MenuBar alignFrameMenuBar = new MenuBar(); + + Menu fileMenu = new Menu("File"); + + MenuItem loadApplication = new MenuItem("View in Full Application"); + + MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + + MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ..."); + + MenuItem outputFeatures = new MenuItem("Export Features ..."); + + MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + MenuItem closeMenuItem = new MenuItem("Close"); + + Menu editMenu = new Menu("Edit"); + + Menu viewMenu = new Menu("View"); + + Menu colourMenu = new Menu("Colour"); + + Menu calculateMenu = new Menu("Calculate"); + + MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + + MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + + MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + + MenuItem remove2LeftMenuItem = new MenuItem(); + + MenuItem remove2RightMenuItem = new MenuItem(); + + MenuItem removeGappedColumnMenuItem = new MenuItem(); + + MenuItem removeAllGapsMenuItem = new MenuItem(); + + CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + + MenuItem sortPairwiseMenuItem = new MenuItem(); + + MenuItem sortIDMenuItem = new MenuItem(); + + MenuItem sortGroupMenuItem = new MenuItem(); + + MenuItem removeRedundancyMenuItem = new MenuItem(); + + MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + + MenuItem PCAMenuItem = new MenuItem(); + + MenuItem averageDistanceTreeMenuItem = new MenuItem(); + + MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); - Menu outputTextboxMenu = new Menu(); - MenuItem clustalColour = new MenuItem(); - MenuItem zappoColour = new MenuItem(); - MenuItem taylorColour = new MenuItem(); - MenuItem hydrophobicityColour = new MenuItem(); - MenuItem helixColour = new MenuItem(); - MenuItem strandColour = new MenuItem(); - MenuItem turnColour = new MenuItem(); - MenuItem buriedColour = new MenuItem(); - MenuItem userDefinedColour = new MenuItem(); - MenuItem PIDColour = new MenuItem(); - MenuItem BLOSUM62Colour = new MenuItem(); + + Menu outputTextboxMenu = new Menu(); + + MenuItem clustalColour = new MenuItem(); + + MenuItem zappoColour = new MenuItem(); + + MenuItem taylorColour = new MenuItem(); + + MenuItem hydrophobicityColour = new MenuItem(); + + MenuItem helixColour = new MenuItem(); + + MenuItem strandColour = new MenuItem(); + + MenuItem turnColour = new MenuItem(); + + MenuItem buriedColour = new MenuItem(); + + MenuItem userDefinedColour = new MenuItem(); + + MenuItem PIDColour = new MenuItem(); + + MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem alProperties = new MenuItem("Alignment Properties..."); + + CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem(); + + MenuItem alProperties = new MenuItem("Alignment Properties..."); + MenuItem overviewMenuItem = new MenuItem(); - MenuItem undoMenuItem = new MenuItem(); - MenuItem redoMenuItem = new MenuItem(); - CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + + MenuItem undoMenuItem = new MenuItem(); + + MenuItem redoMenuItem = new MenuItem(); + + CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); - CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + + CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); - CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - MenuItem nucleotideColour = new MenuItem(); + + CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + + MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); - CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - MenuItem font = new MenuItem(); - CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + + CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + + MenuItem font = new MenuItem(); + + CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + + CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + + CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); - CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - Menu sortByTreeMenu = new Menu(); + + CheckboxMenuItem autoCalculate = new CheckboxMenuItem( + "Autocalculate Consensus", true); + + Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); - CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - Panel embeddedMenu; - Label embeddedEdit; - Label embeddedSelect; - Label embeddedView; - Label embeddedFormat; - Label embeddedColour; - Label embeddedFile; - Label embeddedHelp; - Label embeddedCalculate; - FlowLayout flowLayout1; - - private void jbInit() - throws Exception + + CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + + CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem(); + + CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem(); + + private void jbInit() throws Exception { setMenuBar(alignFrameMenuBar); @@ -2434,11 +2622,11 @@ public class AlignFrame MenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; - i++) + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { - item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + item = new MenuItem( + jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { @@ -2486,8 +2674,8 @@ public class AlignFrame pairwiseAlignmentMenuItem.addActionListener(this); PCAMenuItem.setLabel("Principal Component Analysis"); PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); + averageDistanceTreeMenuItem + .setLabel("Average Distance Using % Identity"); averageDistanceTreeMenuItem.addActionListener(this); neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); neighbourTreeMenuItem.addActionListener(this); @@ -2518,8 +2706,8 @@ public class AlignFrame PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62 Score"); BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem + .setLabel("Average Distance Using BLOSUM62"); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); njTreeBlosumMenuItem.addActionListener(this); @@ -2527,6 +2715,8 @@ public class AlignFrame annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); colourTextMenuItem.addItemListener(this); + displayNonconservedMenuItem.setLabel("Show non-conserved"); + displayNonconservedMenuItem.addItemListener(this); alProperties.addActionListener(this); overviewMenuItem.setLabel("Overview Window"); overviewMenuItem.addActionListener(this); @@ -2591,7 +2781,10 @@ public class AlignFrame 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); @@ -2668,6 +2861,7 @@ public class AlignFrame viewMenu.add(menu1); viewMenu.add(menu2); viewMenu.addSeparator(); + viewMenu.add(followMouseOverFlag); viewMenu.add(annotationPanelMenuItem); viewMenu.addSeparator(); viewMenu.add(sequenceFeatures); @@ -2729,7 +2923,9 @@ public class AlignFrame 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); @@ -2739,152 +2935,79 @@ public class AlignFrame selectMenu.add(deleteGroups); } - public void setEmbedded() - { - - embeddedMenu = new Panel(); - embeddedEdit = new Label("Edit"); - embeddedSelect = new Label("Select"); - embeddedView = new Label("View"); - embeddedFormat = new Label("Format"); - embeddedColour = new Label("Colour"); - embeddedFile = new Label("File"); - embeddedHelp = new Label("Help"); - embeddedCalculate = new Label("Calculate"); - flowLayout1 = new FlowLayout(); - embeddedMenu.setBackground(Color.lightGray); - embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedMenu.add(embeddedFile); - embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSelect); - embeddedMenu.add(embeddedView); - embeddedMenu.add(embeddedFormat); - embeddedMenu.add(embeddedColour); - embeddedMenu.add(embeddedCalculate); - embeddedMenu.add(embeddedHelp); - flowLayout1.setAlignment(FlowLayout.LEFT); - flowLayout1.setHgap(2); - flowLayout1.setVgap(0); - embeddedFile.addMouseListener(this); - embeddedEdit.addMouseListener(this); - embeddedSelect.addMouseListener(this); - embeddedView.addMouseListener(this); - embeddedFormat.addMouseListener(this); - embeddedColour.addMouseListener(this); - embeddedCalculate.addMouseListener(this); - embeddedHelp.addMouseListener(this); - - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Seperator - - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - - alignPanel.setSize(viewport.applet.getSize().width, - viewport.applet.getSize().height - - embeddedMenu.HEIGHT - statusBar.HEIGHT); - - viewport.applet.add(alignPanel, BorderLayout.CENTER); - viewport.applet.validate(); - - } - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + Menu formatMenu = new Menu(); - Menu selectMenu = new Menu(); - MenuItem newView = new MenuItem(); - public void mousePressed(MouseEvent evt) - { - PopupMenu popup = null; - Label source = (Label) evt.getSource(); - if (source == embeddedFile) - { - popup = filePopup = genPopupMenu(filePopup, fileMenu); - } - else if (source == embeddedEdit) - { - popup = editPopup = genPopupMenu(editPopup, editMenu); - } - else if (source == embeddedSelect) - { - popup = searchPopup = genPopupMenu(searchPopup, selectMenu); - } - else if (source == embeddedView) - { - popup = viewPopup = genPopupMenu(viewPopup, viewMenu); - } - else if (source == embeddedFormat) - { - popup = formatPopup = genPopupMenu(formatPopup, formatMenu); - } - else if (source == embeddedColour) - { - popup = colourPopup = genPopupMenu(colourPopup, colourMenu); - } - else if (source == embeddedCalculate) - { - popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); - } - else if (source == embeddedHelp) - { - popup = helpPopup = genPopupMenu(helpPopup, helpMenu); - } + Menu selectMenu = new Menu(); - embeddedMenu.add(popup); - popup.show(embeddedMenu, - source.getBounds().x, - source.getBounds().y + source.getBounds().getSize().height); - } + MenuItem newView = new MenuItem(); - PopupMenu genPopupMenu(PopupMenu popup, Menu original) - { - if (popup != null) - { - return popup; + /** + * 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); + viewport.applet.validate(); } - popup = new PopupMenu(); - int m, mSize = original.getItemCount(); - for (m = 0; m < mSize; m++) + else { - popup.add(original.getItem(m)); - mSize--; - m--; + // ////// + // 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); } - - return popup; } - - public void mouseClicked(MouseEvent evt) - {} - - public void mouseReleased(MouseEvent evt) - {} - - public void mouseEntered(MouseEvent evt) - {} - - public void mouseExited(MouseEvent evt) - {} - }