X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4ee6e27390379e29054637fe6b614cb06fd51109;hb=1a6f14e0fe4826e8232ae7edd6767cd5d95fbbae;hp=2b53d7672379948c423b3f0ca158c2fe8e183c4a;hpb=0c0f58648af5512096275b634158c37c87989eaa;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 2b53d76..4ee6e27 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -19,62 +19,73 @@ package jalview.appletgui; -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; +import java.io.*; +import java.net.*; +import java.util.*; + import java.awt.*; import java.awt.event.*; -import java.util.*; -import java.io.InputStreamReader; -import java.io.BufferedReader; -import java.net.URL; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; -public class AlignFrame extends Frame implements ActionListener, +public class AlignFrame + extends Frame implements ActionListener, ItemListener, KeyListener, MouseListener { public AlignmentPanel alignPanel; public AlignViewport viewport; - int NEW_WINDOW_WIDTH = 700; - int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + 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) { - jalviewServletURL = applet.getParameter("APPLICATION_URL"); + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } - try{ + try + { jbInit(); - }catch(Exception ex) + } + catch (Exception ex) { ex.printStackTrace(); } - this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + annotationPanelMenuItem.setState(viewport.showAnnotation); seqLimits.setState(viewport.showJVSuffix); - if(applet!=null) + if (applet != null) { String param = applet.getParameter("sortBy"); if (param != null) { if (param.equalsIgnoreCase("Id")) + { sortIDMenuItem_actionPerformed(); + } else if (param.equalsIgnoreCase("Pairwise Identity")) + { sortPairwiseMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -93,13 +104,13 @@ public class AlignFrame extends Frame implements ActionListener, if (param != null) { int width = Integer.parseInt(param); - NEW_WINDOW_WIDTH = width; + DEFAULT_WIDTH = width; } param = applet.getParameter("windowHeight"); if (param != null) { int height = Integer.parseInt(param); - NEW_WINDOW_HEIGHT = height; + DEFAULT_HEIGHT = height; } } catch (Exception ex) @@ -107,37 +118,28 @@ public class AlignFrame extends Frame implements ActionListener, } - //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); + //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); - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() + if (embedded) { - public void propertyChange(java.beans.PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - - - if(embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - alignPanel.validate(); - alignPanel.repaint(); + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + alignPanel.validate(); + alignPanel.paintAlignment(true); } + public AlignViewport getAlignViewport() { return viewport; @@ -148,7 +150,6 @@ public class AlignFrame extends Frame implements ActionListener, return alignPanel.seqPanel.seqCanvas; } - /** * DOCUMENT ME! * @@ -159,39 +160,46 @@ public class AlignFrame extends Frame implements ActionListener, { 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); + try + { + featuresFile = new jalview.io.FeaturesFile(file, + type).parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas. + getFeatureRenderer().featureColours, + featureLinks, + true); } - catch(Exception ex) + catch (Exception ex) { ex.printStackTrace(); } - if(featuresFile) + if (featuresFile) { - if(featureLinks.size()>0) + if (featureLinks.size() > 0) + { alignPanel.seqPanel.seqCanvas .getFeatureRenderer().featureLinks = featureLinks; + } viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } } - public void keyPressed(KeyEvent evt) { - if (viewport.cursorMode - && evt.getKeyCode() >= KeyEvent.VK_0 - && evt.getKeyCode() <= KeyEvent.VK_9) - { - 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()) { @@ -215,9 +223,9 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_V: - if (evt.isControlDown() || evt.isMetaDown()) + if (evt.isControlDown()) { - paste(true); + paste(evt.isShiftDown()); } break; case KeyEvent.VK_A: @@ -227,50 +235,62 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - if(viewport.cursorMode) + if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0,1); + alignPanel.seqPanel.moveCursor(0, 1); } else + { moveSelectedSequences(false); + } break; case KeyEvent.VK_UP: if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0,-1); + alignPanel.seqPanel.moveCursor(0, -1); } else + { moveSelectedSequences(true); + } break; case KeyEvent.VK_LEFT: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(-1,0); - } + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( -1, 0); break; case KeyEvent.VK_RIGHT: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(1,0); - } - break; + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( 1, 0); + break; + case KeyEvent.VK_SPACE: - if(viewport.cursorMode) + if (viewport.cursorMode) { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown() + ); } break; case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: - if(viewport.cursorMode) + if (viewport.cursorMode) { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown()); } - else + else { cut_actionPerformed(); alignPanel.seqPanel.seqCanvas.repaint(); @@ -278,13 +298,13 @@ public class AlignFrame extends Frame implements ActionListener, break; case KeyEvent.VK_S: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRow(); } break; case KeyEvent.VK_P: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorPosition(); } @@ -292,36 +312,35 @@ public class AlignFrame extends Frame implements ActionListener, case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: - if(viewport.cursorMode) + 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; - } - alignPanel.seqPanel.seqCanvas.repaint(); - 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()) @@ -329,165 +348,489 @@ public class AlignFrame extends Frame implements ActionListener, findMenuItem_actionPerformed(); } break; + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) + { + viewport.showAllHiddenSeqs(); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + viewport.showAllHiddenColumns(); + } + } + break; + } + + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, + viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + + case KeyEvent.VK_Z: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + if (evt.isControlDown()) + { + if (evt.isShiftDown()) + { + this.removeAllGapsMenuItem_actionPerformed(); + } + else + { + removeGappedColumnMenuItem_actionPerformed(); + } + } + break; + case KeyEvent.VK_I: + if (evt.isControlDown()) + { + if (evt.isAltDown()) + { + viewport.invertColumnSelection(); + } + else + { + this.invertSequenceMenuItem_actionPerformed(); + } + } + break; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; + } + alignPanel.paintAlignment(true); } + public void keyReleased(KeyEvent evt) {} + public void keyTyped(KeyEvent evt) {} -public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==colourTextMenuItem) - colourTextMenuItem_actionPerformed(); - else if(evt.getSource()==wrapMenuItem) - wrapMenuItem_actionPerformed(); - else if(evt.getSource()==scaleAbove) - scaleAbove_actionPerformed(); - else if(evt.getSource()==scaleLeft) - scaleLeft_actionPerformed(); - else if(evt.getSource()==scaleRight) - scaleRight_actionPerformed(); - else if(evt.getSource()==seqLimits) + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == colourTextMenuItem) + { + colourTextMenuItem_actionPerformed(); + } + else if (evt.getSource() == wrapMenuItem) + { + wrapMenuItem_actionPerformed(); + } + else if (evt.getSource() == scaleAbove) + { + viewport.setScaleAboveWrapped(scaleAbove.getState()); + } + else if (evt.getSource() == scaleLeft) + { + viewport.setScaleLeftWrapped(scaleLeft.getState()); + } + else if (evt.getSource() == scaleRight) + { + viewport.setScaleRightWrapped(scaleRight.getState()); + } + else if (evt.getSource() == seqLimits) + { seqLimits_itemStateChanged(); - else if(evt.getSource()==viewBoxesMenuItem) - viewBoxesMenuItem_actionPerformed(); - else if(evt.getSource()==viewTextMenuItem) - viewTextMenuItem_actionPerformed(); - else if(evt.getSource()==renderGapsMenuItem) - renderGapsMenuItem_actionPerformed(); - else if(evt.getSource()==annotationPanelMenuItem) - annotationPanelMenuItem_actionPerformed(); - 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) - applyToAllGroups_actionPerformed(); - else if(evt.getSource()==autoCalculate) - viewport.autocalculateConsensus = autoCalculate.getState(); - } - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==inputText) + } + else if (evt.getSource() == viewBoxesMenuItem) + { + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + } + else if (evt.getSource() == viewTextMenuItem) + { + viewport.setShowText(viewTextMenuItem.getState()); + } + else if (evt.getSource() == renderGapsMenuItem) + { + viewport.setRenderGaps(renderGapsMenuItem.getState()); + } + else if (evt.getSource() == annotationPanelMenuItem) + { + viewport.setShowAnnotation(annotationPanelMenuItem.getState()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + } + else if (evt.getSource() == sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if (evt.getSource() == conservationMenuItem) + { + conservationMenuItem_actionPerformed(); + } + else if (evt.getSource() == abovePIDThreshold) + { + abovePIDThreshold_actionPerformed(); + } + else if (evt.getSource() == applyToAllGroups) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + } + else if (evt.getSource() == autoCalculate) + { + viewport.autocalculateConsensus = autoCalculate.getState(); + } + + alignPanel.paintAlignment(true); + } + + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if (source == inputText) + { inputText_actionPerformed(); - else if(evt.getSource()==loadTree) + } + else if (source == loadTree) + { loadTree_actionPerformed(); - else if(evt.getSource()==loadApplication) + } + else if (source == loadApplication) + { launchFullApplication(); - else if(evt.getSource()==closeMenuItem) + } + 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(evt.getSource()==copy) + } + else if (source == copy) + { copy_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + } + else if (source == undoMenuItem) + { undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + } + else if (source == redoMenuItem) + { redoMenuItem_actionPerformed(); - else if(evt.getSource()==inputText) - inputText_actionPerformed(); - else if(evt.getSource()==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(evt.getSource()==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(evt.getSource()==copy) - copy_actionPerformed(); - else if(evt.getSource()==pasteNew) - pasteNew_actionPerformed(); - else if(evt.getSource()==pasteThis) - pasteThis_actionPerformed(); - else if(evt.getSource()==cut) - cut_actionPerformed(); - else if(evt.getSource()==delete) - delete_actionPerformed(); - else if(evt.getSource()==deleteGroups) - deleteGroups_actionPerformed(); - else if(evt.getSource()==selectAllSequenceMenuItem) - selectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==deselectAllSequenceMenuItem) - deselectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==invertSequenceMenuItem) - invertSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==remove2LeftMenuItem) - remove2LeftMenuItem_actionPerformed(); - else if(evt.getSource()==remove2RightMenuItem) - remove2RightMenuItem_actionPerformed(); - else if(evt.getSource()==removeGappedColumnMenuItem) - removeGappedColumnMenuItem_actionPerformed(); - else if(evt.getSource()==removeAllGapsMenuItem) - removeAllGapsMenuItem_actionPerformed(); - else if(evt.getSource()==findMenuItem) - findMenuItem_actionPerformed(); - else if(evt.getSource()==font) - font_actionPerformed(); - else if(evt.getSource()==featureSettings) - featureSettings_actionPerformed(); - else if(evt.getSource()==overviewMenuItem) - overviewMenuItem_actionPerformed(); - else if(evt.getSource()==noColourmenuItem) - noColourmenuItem_actionPerformed(); - else if(evt.getSource()==clustalColour) - clustalColour_actionPerformed(); - else if(evt.getSource()==zappoColour) - zappoColour_actionPerformed(); - else if(evt.getSource()==taylorColour) - taylorColour_actionPerformed(); - else if(evt.getSource()==hydrophobicityColour) - hydrophobicityColour_actionPerformed(); - else if(evt.getSource()==helixColour) - helixColour_actionPerformed(); - else if(evt.getSource()==strandColour) - strandColour_actionPerformed(); - else if(evt.getSource()==turnColour) - turnColour_actionPerformed(); - else if(evt.getSource()==buriedColour) - buriedColour_actionPerformed(); - else if(evt.getSource()==nucleotideColour) - nucleotideColour_actionPerformed(); - else if(evt.getSource()==modifyPID) - modifyPID_actionPerformed(); - else if(evt.getSource()==modifyConservation) - modifyConservation_actionPerformed(); - else if(evt.getSource()==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(evt.getSource()==PIDColour) - PIDColour_actionPerformed(); - else if(evt.getSource()==BLOSUM62Colour) - BLOSUM62Colour_actionPerformed(); - else if(evt.getSource()==annotationColour) - new AnnotationColourChooser(viewport, alignPanel); - else if(evt.getSource()==sortPairwiseMenuItem) - sortPairwiseMenuItem_actionPerformed(); - else if(evt.getSource()==sortIDMenuItem) - sortIDMenuItem_actionPerformed(); - else if(evt.getSource()==sortGroupMenuItem) - sortGroupMenuItem_actionPerformed(); - else if(evt.getSource()==removeRedundancyMenuItem) - removeRedundancyMenuItem_actionPerformed(); - else if(evt.getSource()==pairwiseAlignmentMenuItem) - pairwiseAlignmentMenuItem_actionPerformed(); - else if(evt.getSource()==PCAMenuItem) - PCAMenuItem_actionPerformed(); - else if(evt.getSource()==averageDistanceTreeMenuItem) - averageDistanceTreeMenuItem_actionPerformed(); - else if(evt.getSource()==neighbourTreeMenuItem) - neighbourTreeMenuItem_actionPerformed(); - else if(evt.getSource()==njTreeBlosumMenuItem) - njTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==avDistanceTreeBlosumMenuItem) - avTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==documentation) - documentation_actionPerformed(); - else if(evt.getSource()==about) - about_actionPerformed(); - - } + } + else if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == pasteNew) + { + pasteNew_actionPerformed(); + } + else if (source == pasteThis) + { + pasteThis_actionPerformed(); + } + else if (source == cut) + { + cut_actionPerformed(); + } + else if (source == delete) + { + delete_actionPerformed(); + } + else if (source == deleteGroups) + { + deleteGroups_actionPerformed(); + } + else if (source == selectAllSequenceMenuItem) + { + selectAllSequenceMenuItem_actionPerformed(); + } + else if (source == deselectAllSequenceMenuItem) + { + deselectAllSequenceMenuItem_actionPerformed(); + } + else if (source == invertSequenceMenuItem) + { + invertSequenceMenuItem_actionPerformed(); + } + else if (source == invertColSel) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + } + else if (source == remove2LeftMenuItem) + { + trimAlignment(true); + } + else if (source == remove2RightMenuItem) + { + trimAlignment(false); + } + else if (source == removeGappedColumnMenuItem) + { + removeGappedColumnMenuItem_actionPerformed(); + } + else if (source == removeAllGapsMenuItem) + { + removeAllGapsMenuItem_actionPerformed(); + } + else if (source == findMenuItem) + { + findMenuItem_actionPerformed(); + } + else if (source == font) + { + new FontChooser(alignPanel); + } + else if (source == newView) + { + newView(); + } + else if (source == showColumns) + { + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); + } + else if (source == showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if (source == hideColumns) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + else if (source == hideSequences && viewport.getSelectionGroup() != null) + { + viewport.hideAllSelectedSeqs(); + } + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if (source == 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 == 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() { @@ -499,93 +842,178 @@ public void itemStateChanged(ItemEvent evt) protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + 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().getSequences(), - viewport.showJVSuffix)); + 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()); + + 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; + } + + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + if (format.equalsIgnoreCase("Jalview")) + { + features = new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + else + { + features = new FeaturesFile().printGFFFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + + 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( applet.getParameter("file") ) ); + 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(applet.getParameter("features")!=null) + if (viewport.applet.getParameter("annotations") != null) { - url.append( "&features=" ); - url.append( appendProtocol( applet.getParameter("features") ) ); + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if(applet.getParameter("defaultColour")!=null) + 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(applet.getParameter("defaultColour")) + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) ); } - if(applet.getParameter("userDefinedColour")!=null) + if (viewport.applet.getParameter("userDefinedColour") != null) { - url.append( "&colour=" + - removeWhiteSpace( applet.getParameter("userDefinedColour") ) - ); + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter( + "userDefinedColour")) + ); } 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); - }catch(java.net.MalformedURLException ex) + try + { + new URL(url); + } + catch (java.net.MalformedURLException ex) { - url = applet.getCodeBase()+url; + url = viewport.applet.getCodeBase() + url; } return url; } public void closeMenuItem_actionPerformed() { - PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && applet==null) + 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(); } - Stack historyList = new Stack(); - Stack redoList = new Stack(); - + /** + * DOCUMENT ME! + */ void updateEditMenuBar() { - if (historyList.size() > 0) + + if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setLabel("Undo " + command.getDescription()); } else { @@ -593,11 +1021,12 @@ public void itemStateChanged(ItemEvent evt) undoMenuItem.setLabel("Undo"); } - if (redoList.size() > 0) + if (viewport.redoList.size() > 0) { redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setLabel("Redo " + command.getDescription()); } else { @@ -606,37 +1035,104 @@ public void itemStateChanged(ItemEvent evt) } } - public void addHistoryItem(HistoryItem hi) + public void addHistoryItem(CommandI command) { - historyList.push(hi); - updateEditMenuBar(); + 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() { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + if (viewport.historyList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void redoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); + if (viewport.redoList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + AlignViewport getOriginatingSource(CommandI command) { - hi.restore(); + 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; + } + } + } + } - updateEditMenuBar(); + 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; + } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + return originalSource; } public void moveSelectedSequences(boolean up) @@ -652,13 +1148,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -672,13 +1168,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(true).contains(seq)) + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(true).contains(temp)) + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) { continue; } @@ -688,10 +1184,100 @@ public void itemStateChanged(ItemEvent evt) } } - alignPanel.repaint(); + 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(); } - StringBuffer copiedSequences; + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -702,7 +1288,7 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -712,52 +1298,72 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(false); i++) + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) { - SequenceI seq = 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); - while (seq == null) + 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 + "")) { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; - break; - } - else - { - index++; - } + break; + } + else + { + index++; } + } - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); + //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; + //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++) + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } + endRes++; } + } - if(endRes>0) - { - endRes += seq.getStart() -1; - } + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); } } @@ -769,8 +1375,6 @@ public void itemStateChanged(ItemEvent evt) protected void pasteThis_actionPerformed() { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); paste(false); } @@ -778,6 +1382,7 @@ public void itemStateChanged(ItemEvent evt) { try { + if (copiedSequences == null) { return; @@ -790,26 +1395,16 @@ public void itemStateChanged(ItemEvent evt) String name = st.nextToken(); int start = Integer.parseInt(st.nextToken()); int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, end); - - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.addElement(sequence); - } + 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) { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { @@ -820,18 +1415,24 @@ public void itemStateChanged(ItemEvent evt) newtitle = newtitle.concat("- from " + getTitle()); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), - applet, + 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, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); + jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); } else { - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + addSequences(newSeqs); } } @@ -840,6 +1441,30 @@ public void itemStateChanged(ItemEvent evt) } + 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(); @@ -848,65 +1473,63 @@ public void itemStateChanged(ItemEvent evt) protected void delete_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) { return; } - - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.getSize(false)==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.getSize(false); i++) + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - // If the cut affects all sequences, remove highlighted columns - if (allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } + 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); + } - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } + 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.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) { - try - { - this.setVisible(false); - } - catch (Exception ex) - {} + this.setVisible(false); } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; viewport.setSelectionGroup(null); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void selectAllSequenceMenuItem_actionPerformed() @@ -916,26 +1539,26 @@ public void itemStateChanged(ItemEvent evt) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth()-1); + sg.setEndRes(viewport.alignment.getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } public void deselectAllSequenceMenuItem_actionPerformed() { - if(viewport.cursorMode) + if (viewport.cursorMode) { - alignPanel.seqPanel.keyboardNo1=null; - alignPanel.seqPanel.keyboardNo2=null; + 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.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } public void invertSequenceMenuItem_actionPerformed() @@ -946,243 +1569,240 @@ public void itemStateChanged(ItemEvent evt) sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); } - PaintRefresher.Refresh(null, viewport.alignment); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } - public void remove2LeftMenuItem_actionPerformed() + void trimAlignment(boolean trimLeft) { ColumnSelection colSel = viewport.getColumnSelection(); + int column; + if (colSel.size() > 0) { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - viewport.getSelectionGroup().adjustForRemoveLeft(min); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) + else { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } + seqs = viewport.alignment.getSequencesArray(); } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - public void remove2RightMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - if (viewport.getSelectionGroup() != null) + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); + } + else { - viewport.getSelectionGroup().adjustForRemoveRight(max); + 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 (!sg.adjustForRemoveRight(max)) + + 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()); + } } public void removeGappedColumnMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); + 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()); - viewport.getAlignment().removeGaps(); - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); + 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); - SequenceI current; - int jSize; + addHistoryItem(new RemoveGapsCommand("Remove Gaps", + seqs, + start, end, + viewport.alignment)); - Vector seqs=null; + viewport.setStartRes(seq.findIndex(startRes) - 1); - int start=0, end = viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSequences(false) != null - && viewport.getSelectionGroup().getSize(false)>0) + } + + public void findMenuItem_actionPerformed() + { + new Finder(alignPanel); + } + + public void newView() + { + AlignmentI newal; + if (viewport.hasHiddenRows) { - seqs = viewport.getSelectionGroup().getSequences(true); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; + newal = new Alignment(viewport.getAlignment(). + getHiddenSequences() + .getFullAlignment(). + getSequencesArray()); } else - seqs = viewport.alignment.getSequences(); - - for (int i = 0; i < seqs.size(); i++) { - current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); - - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; + newal = new Alignment(viewport.alignment.getSequencesArray()); + } - do + if (viewport.alignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - if(rangeStart==-1) - { - rangeStart = j; - rangeEnd = j+1; - } - else - { - rangeEnd++; - } - j++; - } - else + if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) { - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - j-=rangeEnd-rangeStart; - jSize-=rangeEnd-rangeStart; - rangeStart = -1; - rangeEnd = -1; - } - else - j++; + newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); } } - while (j < end && j < jSize); - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - } } - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - public void alignmentChanged() - { - viewport.alignment.padGaps(); - if(viewport.autocalculateConsensus) - { - viewport.updateConsensus(); - viewport.updateConservation(); - } + AlignFrame newaf = new AlignFrame(newal, + viewport.applet, + "", + false); - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); + newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); - viewport.alignment.adjustSequenceAnnotations(); - alignPanel.repaint(); - } + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); - void resetAllColourSchemes() - { - ColourSchemeI cs = viewport.globalColourScheme; - if(cs!=null) + Vector comps = (Vector) PaintRefresher.components.get(viewport. + getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) { - if (cs instanceof ClustalxColourScheme) + if (comps.elementAt(i) instanceof AlignmentPanel) { - ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); - } - - cs.setConsensus(viewport.vconsensus); - if (cs.conservationApplied()) - { - 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); + viewSize++; } } - int s, sSize = viewport.alignment.getGroups().size(); - for(s=0; s -1) { - SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); - if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) - { - ((ClustalxColourScheme)sg.cs).resetClustalX( - sg.getSequences(true), sg.getWidth()); - } - sg.recalcConservation(); + title = title.substring(0, title.indexOf("(View")); } - } + title += "(View " + viewSize + ")"; + newaf.setTitle(title.toString()); - public void findMenuItem_actionPerformed() - { - new Finder(alignPanel); - } + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; - public void font_actionPerformed() - { - new FontChooser(alignPanel); } - public void seqLimits_itemStateChanged() { viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } protected void wrapMenuItem_actionPerformed() @@ -1192,54 +1812,7 @@ public void itemStateChanged(ItemEvent evt) scaleAbove.setEnabled(wrapMenuItem.getState()); scaleLeft.setEnabled(wrapMenuItem.getState()); scaleRight.setEnabled(wrapMenuItem.getState()); - alignPanel.repaint(); - } - - protected void scaleAbove_actionPerformed() - { - viewport.setScaleAboveWrapped(scaleAbove.getState()); - alignPanel.repaint(); - } - - protected void scaleLeft_actionPerformed() - { - viewport.setScaleLeftWrapped(scaleLeft.getState()); - alignPanel.repaint(); - } - - protected void scaleRight_actionPerformed() - { - viewport.setScaleRightWrapped(scaleRight.getState()); - alignPanel.repaint(); - } - - public void viewBoxesMenuItem_actionPerformed() - { - viewport.setShowBoxes(viewBoxesMenuItem.getState()); - alignPanel.repaint(); - } - - public void viewTextMenuItem_actionPerformed() - { - viewport.setShowText(viewTextMenuItem.getState()); - alignPanel.repaint(); - } - - protected void renderGapsMenuItem_actionPerformed() - { - viewport.setRenderGaps(renderGapsMenuItem.getState()); - alignPanel.repaint(); - } - - public void annotationPanelMenuItem_actionPerformed() - { - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); - } - - public void featureSettings_actionPerformed() - { - new FeatureSettings(viewport, alignPanel); + alignPanel.paintAlignment(true); } public void overviewMenuItem_actionPerformed() @@ -1254,8 +1827,8 @@ public void itemStateChanged(ItemEvent evt) frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.preferredSize().width, - overview.preferredSize().height + 50); + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); frame.pack(); frame.addWindowListener(new WindowAdapter() @@ -1270,68 +1843,11 @@ public void itemStateChanged(ItemEvent evt) } - protected void noColourmenuItem_actionPerformed() - { - changeColour(null); - } - - public void clustalColour_actionPerformed() - { - abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), - viewport.alignment.getWidth())); - } - - public void zappoColour_actionPerformed() - { - changeColour(new ZappoColourScheme()); - } - - public void taylorColour_actionPerformed() - { - changeColour(new TaylorColourScheme()); - } - - public void hydrophobicityColour_actionPerformed() - { - changeColour(new HydrophobicColourScheme()); - } - - public void helixColour_actionPerformed() - { - changeColour(new HelixColourScheme()); - } - - public void strandColour_actionPerformed() - { - changeColour(new StrandColourScheme()); - } - - public void turnColour_actionPerformed() - { - changeColour(new TurnColourScheme()); - } - - public void buriedColour_actionPerformed() - { - changeColour(new BuriedColourScheme()); - } - - public void nucleotideColour_actionPerformed() - { - changeColour(new NucleotideColourScheme()); - } - - protected void applyToAllGroups_actionPerformed() - { - viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); - } - void changeColour(ColourSchemeI cs) { int threshold = 0; - if(cs!=null) + if (cs != null) { if (viewport.getAbovePIDThreshold()) { @@ -1369,7 +1885,7 @@ public void itemStateChanged(ItemEvent evt) cs.setConservation(null); } - cs.setConsensus(viewport.vconsensus); + cs.setConsensus(viewport.hconsensus); } viewport.setGlobalColourScheme(cs); @@ -1381,14 +1897,16 @@ public void itemStateChanged(ItemEvent evt) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if(cs==null) + if (cs == null) { sg.cs = null; continue; } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else { @@ -1408,16 +1926,20 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); + 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(true), 0, + sg.getSequences(viewport. + hiddenRepSequences), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1432,20 +1954,20 @@ public void itemStateChanged(ItemEvent evt) } } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } - alignPanel.repaint(); - } - + 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"); @@ -1455,7 +1977,7 @@ public void itemStateChanged(ItemEvent evt) protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) + if (viewport.getConservationSelected() && viewport.globalColourScheme != null) { SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, "Background"); @@ -1487,55 +2009,42 @@ public void itemStateChanged(ItemEvent evt) modifyPID_actionPerformed(); } - public void userDefinedColour_actionPerformed() - { - new UserDefinedColours(alignPanel, null); - } - - public void PIDColour_actionPerformed() - { - changeColour(new PIDColourScheme()); - } - - public void BLOSUM62Colour_actionPerformed() - { - changeColour(new Blosum62ColourScheme()); - } - public void sortPairwiseMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, - HistoryItem.SORT)); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); - alignPanel.repaint(); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); } public void sortIDMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByID(viewport.getAlignment()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void sortGroupMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByGroup(viewport.getAlignment()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void removeRedundancyMenuItem_actionPerformed() { - new RedundancyPanel(alignPanel); + new RedundancyPanel(alignPanel); } public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize(false) > 1) + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1561,12 +2070,12 @@ public void itemStateChanged(ItemEvent evt) current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) < 4 && - viewport.getSelectionGroup().getSize(false) > 0) + viewport.getSelectionGroup().getSize() < 4 && + viewport.getSelectionGroup().getSize() > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1599,7 +2108,7 @@ public void itemStateChanged(ItemEvent evt) protected void avTreeBlosumMenuItem_actionPerformed() { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } void NewTreePanel(String type, String pwType, String title) @@ -1620,27 +2129,33 @@ public void itemStateChanged(ItemEvent evt) current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - final TreePanel tp = new TreePanel(viewport, - type, - pwType); + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) + { + final TreePanel tp = new TreePanel(viewport, + type, + pwType); - addTreeMenuItem(tp, title); + addTreeMenuItem(tp, title); - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + 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.treeImport = true; - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + 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) @@ -1661,10 +2176,10 @@ public void itemStateChanged(ItemEvent evt) { public void actionPerformed(ActionEvent evt) { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } }); @@ -1685,11 +2200,14 @@ public void itemStateChanged(ItemEvent evt) protected void about_actionPerformed() { - class AboutPanel extends Canvas + class AboutPanel + extends Canvas { String version; public AboutPanel(String version) - { this.version = version; } + { + this.version = version; + } public void paint(Graphics g) { @@ -1701,7 +2219,7 @@ public void itemStateChanged(ItemEvent evt) int y = 5, x = 7; g.setColor(Color.black); g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release "+version, 200, y += fh); + g.drawString("Jalview - Release " + version, 200, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", x, y += fh * 2); @@ -1740,7 +2258,6 @@ public void itemStateChanged(ItemEvent evt) } } - Frame frame = new Frame(); frame.add(new AboutPanel(version)); jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); @@ -1749,7 +2266,7 @@ public void itemStateChanged(ItemEvent evt) public void showURL(String url, String target) { - if (applet == null) + if (viewport.applet == null) { System.out.println("Not running as applet - no browser available."); } @@ -1757,9 +2274,9 @@ public void itemStateChanged(ItemEvent evt) { try { - System.out.println("Show url: "+url); - applet.getAppletContext().showDocument(new java.net.URL(url), - target); + System.out.println("Show url: " + url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), + target); } catch (Exception ex) { @@ -1768,270 +2285,276 @@ public void itemStateChanged(ItemEvent evt) } } - ////////////////////////////////////////////////////////////////////////////////// //JBuilder Graphics here - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu("File"); - protected MenuItem loadApplication = new MenuItem("View in Full Application"); - protected MenuItem loadTree = new MenuItem("Load Associated Tree"); - protected MenuItem closeMenuItem = new MenuItem("Close"); - protected Menu editMenu = new Menu("Edit"); - protected Menu viewMenu = new Menu("View"); - protected Menu colourMenu = new Menu("Colour"); - protected Menu calculateMenu = new Menu("Calculate"); - protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected 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(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - protected 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(); - protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); + protected MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + protected MenuItem loadAnnotations = new MenuItem( + "Load Features/Annotations ..."); + protected MenuItem outputFeatures = new MenuItem("Export Features ..."); + protected MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + protected MenuItem closeMenuItem = new MenuItem("Close"); + protected Menu editMenu = new Menu("Edit"); + protected Menu viewMenu = new Menu("View"); + protected Menu colourMenu = new Menu("Colour"); + protected Menu calculateMenu = new Menu("Calculate"); + protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected 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(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + protected 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(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); Panel embeddedMenu; Label embeddedEdit; - Label embeddedSearch; + Label embeddedSelect; Label embeddedView; + Label embeddedFormat; Label embeddedColour; Label embeddedFile; Label embeddedHelp; Label embeddedCalculate; FlowLayout flowLayout1; - private void jbInit() throws Exception { + private void jbInit() + throws Exception + { - setMenuBar(alignFrameMenuBar); + setMenuBar(alignFrameMenuBar); - MenuItem item; + MenuItem item; - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) - { + // 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 = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. - elementAt( - i)); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); + outputText_actionPerformed(e); + } + }); - outputTextboxMenu.add(item); - } - closeMenuItem.addActionListener(this); - loadApplication.addActionListener(this); - - loadTree.addActionListener(this); - selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - 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); - 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); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); + outputTextboxMenu.add(item); + } + closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); + + loadTree.addActionListener(this); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); seqLimits.setLabel("Show Sequence Limits"); seqLimits.addItemListener(this); featureSettings.setLabel("Feature Settings..."); @@ -2041,132 +2564,163 @@ public void itemStateChanged(ItemEvent evt) sequenceFeatures.setState(false); annotationColour.setLabel("by Annotation..."); annotationColour.addActionListener(this); - + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - if(jalviewServletURL!=null) - fileMenu.add(loadApplication); - fileMenu.addSeparator(); - fileMenu.add(loadTree); - 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(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); + 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(sequenceFeatures); - viewMenu.add(featureSettings); + viewMenu.add(annotationPanelMenuItem); 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); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); colourMenu.add(annotationColour); calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.add(autoCalculate); - this.add(statusBar, BorderLayout.SOUTH); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); } public void setEmbedded() { embeddedMenu = new Panel(); - embeddedEdit = new Label(); - embeddedSearch = new Label(); - embeddedView = new Label(); - embeddedColour = new Label(); - embeddedFile = new Label(); - embeddedHelp = new Label(); - embeddedCalculate = new Label(); + 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.setText("Edit"); embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSearch.setText("Search"); - embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setText("View"); + embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setText("Colour"); + 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)); - embeddedFile.setText("File"); embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setText("Help"); embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setText("Calculate"); embeddedMenu.add(embeddedFile); embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSearch); + embeddedMenu.add(embeddedSelect); embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedFormat); embeddedMenu.add(embeddedColour); embeddedMenu.add(embeddedCalculate); embeddedMenu.add(embeddedHelp); @@ -2175,66 +2729,78 @@ public void itemStateChanged(ItemEvent evt) flowLayout1.setVgap(0); embeddedFile.addMouseListener(this); embeddedEdit.addMouseListener(this); - embeddedSearch.addMouseListener(this); + embeddedSelect.addMouseListener(this); embeddedView.addMouseListener(this); + embeddedFormat.addMouseListener(this); embeddedColour.addMouseListener(this); embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); - // setVisible(false); fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Seperator - applet.setLayout(new BorderLayout()); - applet.add(embeddedMenu, BorderLayout.NORTH); - applet.add(statusBar, BorderLayout.SOUTH); - // applet.validate(); + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); - alignPanel.setSize(applet.size().width, applet.size().height + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); - applet.add(alignPanel, BorderLayout.CENTER); - applet.validate(); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); } - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, colourPopup, calculatePopup, helpPopup; + 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) + Label source = (Label) evt.getSource(); + if (source == embeddedFile) { popup = filePopup = genPopupMenu(filePopup, fileMenu); } - else if(source==embeddedEdit) + else if (source == embeddedEdit) { popup = editPopup = genPopupMenu(editPopup, editMenu); } - else if(source==embeddedSearch) + else if (source == embeddedSelect) { - popup = searchPopup = genPopupMenu(searchPopup, searchMenu); + popup = searchPopup = genPopupMenu(searchPopup, selectMenu); } - else if(source==embeddedView) + else if (source == embeddedView) { popup = viewPopup = genPopupMenu(viewPopup, viewMenu); } - else if(source==embeddedColour) + else if (source == embeddedFormat) + { + popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + } + else if (source == embeddedColour) { popup = colourPopup = genPopupMenu(colourPopup, colourMenu); } - else if(source==embeddedCalculate) + else if (source == embeddedCalculate) { popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); } - else if(source==embeddedHelp) + else if (source == embeddedHelp) { popup = helpPopup = genPopupMenu(helpPopup, helpMenu); } @@ -2247,13 +2813,13 @@ public void itemStateChanged(ItemEvent evt) PopupMenu genPopupMenu(PopupMenu popup, Menu original) { - if(popup!=null) + if (popup != null) { return popup; } popup = new PopupMenu(); int m, mSize = original.getItemCount(); - for(m=0; m