-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- *\r
- * This file is part of Jalview.\r
- *\r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- *\r
- * Jalview is distributed in the hope that it will be useful, but\r
- * WITHOUT ANY WARRANTY; without even the implied warranty\r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
- * PURPOSE. See the GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.analysis.AAFrequency;\r
-import jalview.analysis.AlignmentSorter;\r
-import jalview.analysis.Conservation;\r
-import jalview.api.SequenceStructureBinding;\r
-import jalview.bin.JalviewLite;\r
-import jalview.commands.CommandI;\r
-import jalview.commands.EditCommand;\r
-import jalview.commands.OrderCommand;\r
-import jalview.commands.RemoveGapColCommand;\r
-import jalview.commands.RemoveGapsCommand;\r
-import jalview.commands.SlideSequencesCommand;\r
-import jalview.commands.TrimRegionCommand;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.AlignmentOrder;\r
-import jalview.datamodel.ColumnSelection;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceCollectionI;\r
-import jalview.datamodel.SequenceGroup;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.io.AnnotationFile;\r
-import jalview.io.AppletFormatAdapter;\r
-import jalview.io.FeaturesFile;\r
-import jalview.io.TCoffeeScoreFile;\r
-import jalview.schemes.Blosum62ColourScheme;\r
-import jalview.schemes.BuriedColourScheme;\r
-import jalview.schemes.ClustalxColourScheme;\r
-import jalview.schemes.ColourSchemeI;\r
-import jalview.schemes.HelixColourScheme;\r
-import jalview.schemes.HydrophobicColourScheme;\r
-import jalview.schemes.NucleotideColourScheme;\r
-import jalview.schemes.PIDColourScheme;\r
-import jalview.schemes.PurinePyrimidineColourScheme;\r
-import jalview.schemes.RNAHelicesColourChooser;\r
-import jalview.schemes.ResidueProperties;\r
-import jalview.schemes.StrandColourScheme;\r
-import jalview.schemes.TCoffeeColourScheme;\r
-import jalview.schemes.TaylorColourScheme;\r
-import jalview.schemes.TurnColourScheme;\r
-import jalview.schemes.ZappoColourScheme;\r
-import jalview.structure.StructureSelectionManager;\r
-\r
-import java.awt.BorderLayout;\r
-import java.awt.Canvas;\r
-import java.awt.CheckboxMenuItem;\r
-import java.awt.Color;\r
-import java.awt.Font;\r
-import java.awt.FontMetrics;\r
-import java.awt.Frame;\r
-import java.awt.Graphics;\r
-import java.awt.Label;\r
-import java.awt.Menu;\r
-import java.awt.MenuBar;\r
-import java.awt.MenuItem;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.FocusEvent;\r
-import java.awt.event.FocusListener;\r
-import java.awt.event.ItemEvent;\r
-import java.awt.event.ItemListener;\r
-import java.awt.event.KeyEvent;\r
-import java.awt.event.KeyListener;\r
-import java.awt.event.WindowAdapter;\r
-import java.awt.event.WindowEvent;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.net.URL;\r
-import java.net.URLEncoder;\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.List;\r
-import java.util.StringTokenizer;\r
-import java.util.Vector;\r
-\r
-public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
-{\r
- public AlignmentPanel alignPanel;\r
-\r
- public AlignViewport viewport;\r
-\r
- int DEFAULT_WIDTH = 700;\r
-\r
- int DEFAULT_HEIGHT = 500;\r
-\r
- String jalviewServletURL;\r
-\r
-\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
- {\r
- if (applet != null)\r
- {\r
- jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- viewport = new AlignViewport(al, applet);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
-\r
- viewport.updateConservation(alignPanel);\r
- viewport.updateConsensus(alignPanel);\r
-\r
- annotationPanelMenuItem.setState(viewport.showAnnotation);\r
- displayNonconservedMenuItem.setState(viewport.getShowUnconserved());\r
- followMouseOverFlag.setState(viewport.getFollowHighlight());\r
- showGroupConsensus.setState(viewport.isShowGroupConsensus());\r
- showGroupConservation.setState(viewport.isShowGroupConservation());\r
- showConsensusHistogram.setState(viewport.isShowConsensusHistogram());\r
- showSequenceLogo.setState(viewport.isShowSequenceLogo());\r
- normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());\r
-\r
- seqLimits.setState(viewport.showJVSuffix);\r
-\r
- if (applet != null)\r
- {\r
- String param = applet.getParameter("sortBy");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("Id"))\r
- {\r
- sortIDMenuItem_actionPerformed();\r
- }\r
- else if (param.equalsIgnoreCase("Pairwise Identity"))\r
- {\r
- sortPairwiseMenuItem_actionPerformed();\r
- }\r
- else if (param.equalsIgnoreCase("Length"))\r
- {\r
- sortLengthMenuItem_actionPerformed();\r
- }\r
- }\r
-\r
- param = applet.getParameter("wrap");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("true"))\r
- {\r
- wrapMenuItem.setState(true);\r
- wrapMenuItem_actionPerformed();\r
- }\r
- }\r
- param = applet.getParameter("centrecolumnlabels");\r
- if (param != null)\r
- {\r
- centreColumnLabelFlag.setState(true);\r
- centreColumnLabelFlag_stateChanged();\r
- }\r
- try\r
- {\r
- param = applet.getParameter("windowWidth");\r
- if (param != null)\r
- {\r
- int width = Integer.parseInt(param);\r
- DEFAULT_WIDTH = width;\r
- }\r
- param = applet.getParameter("windowHeight");\r
- if (param != null)\r
- {\r
- int height = Integer.parseInt(param);\r
- DEFAULT_HEIGHT = height;\r
- }\r
- } catch (Exception ex)\r
- {\r
- }\r
-\r
- }\r
- if (viewport.getAlignment().isNucleotide())\r
- {\r
- viewport.updateStrucConsensus(alignPanel);\r
- if (viewport.getAlignment().hasRNAStructure())\r
- {\r
- RNAHelixColour.setEnabled(true);\r
- }\r
- else {\r
- RNAHelixColour.setEnabled(false);\r
- }\r
- } else {\r
- RNAHelixColour.setEnabled(false);\r
- purinePyrimidineColour.setEnabled(false);\r
- }\r
- // Some JVMS send keyevents to Top frame or lowest panel,\r
- // Havent worked out why yet. So add to both this frame and seqCanvas for\r
- // now\r
- this.addKeyListener(this);\r
- alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
- alignPanel.idPanel.idCanvas.addKeyListener(this);\r
- alignPanel.scalePanel.addKeyListener(this);\r
- alignPanel.annotationPanel.addKeyListener(this);\r
- alignPanel.annotationPanelHolder.addKeyListener(this);\r
- alignPanel.annotationSpaceFillerHolder.addKeyListener(this);\r
- alignPanel.alabels.addKeyListener(this);\r
- createAlignFrameWindow(embedded, title);\r
-\r
- validate();\r
- alignPanel.adjustAnnotationHeight();\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public AlignViewport getAlignViewport()\r
- {\r
- return viewport;\r
- }\r
-\r
- public SeqCanvas getSeqcanvas()\r
- {\r
- return alignPanel.seqPanel.seqCanvas;\r
- }\r
-\r
- /**\r
- * Load a features file onto the alignment\r
- *\r
- * @param file file URL, content, or other resolvable path\r
- * @param type is protocol for accessing data referred to by file\r
- */\r
-\r
- public boolean parseFeaturesFile(String file, String type)\r
- {\r
- return parseFeaturesFile(file, type, true);\r
- }\r
-\r
- /**\r
- * Load a features file onto the alignment\r
- *\r
- * @param file file URL, content, or other resolvable path\r
- * @param type is protocol for accessing data referred to by file\r
- * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded\r
- * @return true if data parsed as a features file\r
- */\r
- public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
- {\r
- // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.\r
-\r
- Hashtable featureLinks = new Hashtable();\r
- boolean featuresFile = false;\r
- try\r
- {\r
- featuresFile = new jalview.io.FeaturesFile(file, type)\r
- .parse(viewport.getAlignment(),\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
- featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- if (featuresFile)\r
- {\r
- if (featureLinks.size() > 0)\r
- {\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
- }\r
- if (autoenabledisplay)\r
- {\r
- viewport.showSequenceFeatures = true;\r
- sequenceFeatures.setState(true);\r
- }\r
- if (viewport.featureSettings != null)\r
- {\r
- viewport.featureSettings.refreshTable();\r
- }\r
- alignPanel.paintAlignment(true);\r
- statusBar.setText("Successfully added features to alignment.");\r
- }\r
- return featuresFile;\r
- }\r
-\r
- @Override\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- if (viewport.cursorMode\r
- && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
- .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
- .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
- && Character.isDigit(evt.getKeyChar()))\r
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
-\r
- switch (evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- deselectAllSequenceMenuItem_actionPerformed();\r
-\r
- alignPanel.alabels.cancelDrag();\r
- break;\r
- case KeyEvent.VK_X:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- cut_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_C:\r
- if (viewport.cursorMode && !evt.isControlDown())\r
- {\r
- alignPanel.seqPanel.setCursorColumn();\r
- }\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- copy_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_V:\r
- if (evt.isControlDown())\r
- {\r
- paste(evt.isShiftDown());\r
- }\r
- break;\r
- case KeyEvent.VK_A:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- selectAllSequenceMenuItem_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_DOWN:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0, 1);\r
- }\r
- else\r
- {\r
- moveSelectedSequences(false);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_UP:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0, -1);\r
- }\r
- else\r
- {\r
- moveSelectedSequences(true);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_LEFT:\r
- if (evt.isAltDown() || !viewport.cursorMode)\r
- slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
- else\r
- alignPanel.seqPanel.moveCursor(-1, 0);\r
- break;\r
-\r
- case KeyEvent.VK_RIGHT:\r
- if (evt.isAltDown() || !viewport.cursorMode)\r
- slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
- else\r
- alignPanel.seqPanel.moveCursor(1, 0);\r
- break;\r
-\r
- case KeyEvent.VK_SPACE:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
- || evt.isShiftDown() || evt.isAltDown());\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_DELETE:\r
- case KeyEvent.VK_BACK_SPACE:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
- || evt.isShiftDown() || evt.isAltDown());\r
- }\r
- else\r
- {\r
- cut_actionPerformed();\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_S:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRow();\r
- }\r
- break;\r
- case KeyEvent.VK_P:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorPosition();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_ENTER:\r
- case KeyEvent.VK_COMMA:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRowAndColumn();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_Q:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
- }\r
- break;\r
- case KeyEvent.VK_M:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_F2:\r
- viewport.cursorMode = !viewport.cursorMode;\r
- statusBar.setText("Keyboard editing mode is "\r
- + (viewport.cursorMode ? "on" : "off"));\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_F:\r
- if (evt.isControlDown())\r
- {\r
- findMenuItem_actionPerformed();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_H:\r
- {\r
- boolean toggleSeqs = !evt.isControlDown();\r
- boolean toggleCols = !evt.isShiftDown();\r
- toggleHiddenRegions(toggleSeqs, toggleCols);\r
- break;\r
- }\r
-\r
- case KeyEvent.VK_PAGE_UP:\r
- if (viewport.wrapAlignment)\r
- {\r
- alignPanel.scrollUp(true);\r
- }\r
- else\r
- {\r
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
- - viewport.endSeq + viewport.startSeq);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_PAGE_DOWN:\r
- if (viewport.wrapAlignment)\r
- {\r
- alignPanel.scrollUp(false);\r
- }\r
- else\r
- {\r
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
- + viewport.endSeq - viewport.startSeq);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_Z:\r
- if (evt.isControlDown())\r
- {\r
- undoMenuItem_actionPerformed();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_Y:\r
- if (evt.isControlDown())\r
- {\r
- redoMenuItem_actionPerformed();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_L:\r
- if (evt.isControlDown())\r
- {\r
- trimAlignment(true);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_R:\r
- if (evt.isControlDown())\r
- {\r
- trimAlignment(false);\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_E:\r
- if (evt.isControlDown())\r
- {\r
- if (evt.isShiftDown())\r
- {\r
- this.removeAllGapsMenuItem_actionPerformed();\r
- }\r
- else\r
- {\r
- removeGappedColumnMenuItem_actionPerformed();\r
- }\r
- }\r
- break;\r
- case KeyEvent.VK_I:\r
- if (evt.isControlDown())\r
- {\r
- if (evt.isAltDown())\r
- {\r
- invertColSel_actionPerformed();\r
- }\r
- else\r
- {\r
- invertSequenceMenuItem_actionPerformed();\r
- }\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_U:\r
- if (evt.isControlDown())\r
- {\r
- this.deleteGroups_actionPerformed();\r
- }\r
- break;\r
-\r
- case KeyEvent.VK_T:\r
- if (evt.isControlDown())\r
- {\r
- newView(null);\r
- }\r
- break;\r
-\r
- }\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- /**\r
- * called by key handler and the hide all/show all menu items\r
- *\r
- * @param toggleSeqs\r
- * @param toggleCols\r
- */\r
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
- {\r
- boolean hide = false;\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (!toggleSeqs && !toggleCols)\r
- {\r
- // Hide everything by the current selection - this is a hack - we do the\r
- // invert and then hide\r
- // first check that there will be visible columns after the invert.\r
- if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()\r
- .getSelected().size() > 0)\r
- || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
- .getEndRes()))\r
- {\r
- // now invert the sequence set, if required - empty selection implies\r
- // that no hiding is required.\r
- if (sg != null)\r
- {\r
- invertSequenceMenuItem_actionPerformed();\r
- sg = viewport.getSelectionGroup();\r
- toggleSeqs = true;\r
-\r
- }\r
- viewport.expandColSelection(sg, true);\r
- // finally invert the column selection and get the new sequence\r
- // selection and indicate it should be hidden.\r
- invertColSel_actionPerformed();\r
- toggleCols = true;\r
- }\r
- }\r
-\r
- if (toggleSeqs)\r
- {\r
- if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())\r
- {\r
- hide = true;\r
- viewport.hideAllSelectedSeqs();\r
- }\r
- else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))\r
- {\r
- viewport.showAllHiddenSeqs();\r
- }\r
- }\r
-\r
- if (toggleCols)\r
- {\r
- if (viewport.getColumnSelection().getSelected().size() > 0)\r
- {\r
- viewport.hideSelectedColumns();\r
- if (!toggleSeqs)\r
- {\r
- viewport.setSelectionGroup(sg);\r
- }\r
- }\r
- else if (!hide)\r
- {\r
- viewport.showAllHiddenColumns();\r
- }\r
- }\r
- }\r
-\r
- @Override\r
- public void keyReleased(KeyEvent evt)\r
- {\r
- }\r
-\r
- @Override\r
- public void keyTyped(KeyEvent evt)\r
- {\r
- }\r
-\r
- @Override\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == displayNonconservedMenuItem)\r
- {\r
- displayNonconservedMenuItem_actionPerformed();\r
- }\r
- else if (evt.getSource() == colourTextMenuItem)\r
- {\r
- colourTextMenuItem_actionPerformed();\r
- }\r
- else if (evt.getSource() == wrapMenuItem)\r
- {\r
- wrapMenuItem_actionPerformed();\r
- }\r
- else if (evt.getSource() == scaleAbove)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- }\r
- else if (evt.getSource() == scaleLeft)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- }\r
- else if (evt.getSource() == scaleRight)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- }\r
- else if (evt.getSource() == seqLimits)\r
- {\r
- seqLimits_itemStateChanged();\r
- }\r
- else if (evt.getSource() == viewBoxesMenuItem)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- }\r
- else if (evt.getSource() == viewTextMenuItem)\r
- {\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- }\r
- else if (evt.getSource() == renderGapsMenuItem)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- }\r
- else if (evt.getSource() == annotationPanelMenuItem)\r
- {\r
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
- }\r
- else if (evt.getSource() == sequenceFeatures)\r
- {\r
- viewport.showSequenceFeatures(sequenceFeatures.getState());\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- }\r
- else if (evt.getSource() == conservationMenuItem)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- else if (evt.getSource() == abovePIDThreshold)\r
- {\r
- abovePIDThreshold_actionPerformed();\r
- }\r
- else if (evt.getSource() == applyToAllGroups)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- }\r
- else if (evt.getSource() == autoCalculate)\r
- {\r
- viewport.autoCalculateConsensus = autoCalculate.getState();\r
- }\r
- else if (evt.getSource() == sortByTree)\r
- {\r
- viewport.sortByTree = sortByTree.getState();\r
- }\r
- else if (evt.getSource() == this.centreColumnLabelFlag)\r
- {\r
- centreColumnLabelFlag_stateChanged();\r
- }\r
- else if (evt.getSource() == this.followMouseOverFlag)\r
- {\r
- mouseOverFlag_stateChanged();\r
- }\r
- else if (evt.getSource() == showGroupConsensus)\r
- {\r
- showGroupConsensus_actionPerformed();\r
- }\r
- else if (evt.getSource() == showGroupConservation)\r
- {\r
- showGroupConservation_actionPerformed();\r
- }\r
- else if (evt.getSource() == showSequenceLogo)\r
- {\r
- showSequenceLogo_actionPerformed();\r
- }\r
- else if (evt.getSource() == normSequenceLogo)\r
- {\r
- normSequenceLogo_actionPerformed();\r
- }\r
- else if (evt.getSource() == showConsensusHistogram)\r
- {\r
- showConsensusHistogram_actionPerformed();\r
- }\r
- else if (evt.getSource() == applyAutoAnnotationSettings)\r
- {\r
- applyAutoAnnotationSettings_actionPerformed();\r
- }\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- private void mouseOverFlag_stateChanged()\r
- {\r
- viewport.followHighlight = followMouseOverFlag.getState();\r
- // TODO: could kick the scrollTo mechanism to reset view for current\r
- // searchresults.\r
- }\r
-\r
- private void centreColumnLabelFlag_stateChanged()\r
- {\r
- viewport.centreColumnLabels = centreColumnLabelFlag.getState();\r
- this.alignPanel.annotationPanel.repaint();\r
- }\r
-\r
- @Override\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- Object source = evt.getSource();\r
-\r
- if (source == inputText)\r
- {\r
- inputText_actionPerformed();\r
- }\r
- else if (source == loadTree)\r
- {\r
- loadTree_actionPerformed();\r
- }\r
- else if (source == loadApplication)\r
- {\r
- launchFullApplication();\r
- }\r
- else if (source == loadAnnotations)\r
- {\r
- loadAnnotations();\r
- }\r
- else if (source == outputAnnotations)\r
- {\r
- outputAnnotations(true);\r
- }\r
- else if (source == outputFeatures)\r
- {\r
- outputFeatures(true, "Jalview");\r
- }\r
- else if (source == closeMenuItem)\r
- {\r
- closeMenuItem_actionPerformed();\r
- }\r
- else if (source == copy)\r
- {\r
- copy_actionPerformed();\r
- }\r
- else if (source == undoMenuItem)\r
- {\r
- undoMenuItem_actionPerformed();\r
- }\r
- else if (source == redoMenuItem)\r
- {\r
- redoMenuItem_actionPerformed();\r
- }\r
- else if (source == inputText)\r
- {\r
- inputText_actionPerformed();\r
- }\r
- else if (source == closeMenuItem)\r
- {\r
- closeMenuItem_actionPerformed();\r
- }\r
- else if (source == undoMenuItem)\r
- {\r
- undoMenuItem_actionPerformed();\r
- }\r
- else if (source == redoMenuItem)\r
- {\r
- redoMenuItem_actionPerformed();\r
- }\r
- else if (source == copy)\r
- {\r
- copy_actionPerformed();\r
- }\r
- else if (source == pasteNew)\r
- {\r
- pasteNew_actionPerformed();\r
- }\r
- else if (source == pasteThis)\r
- {\r
- pasteThis_actionPerformed();\r
- }\r
- else if (source == cut)\r
- {\r
- cut_actionPerformed();\r
- }\r
- else if (source == delete)\r
- {\r
- delete_actionPerformed();\r
- }\r
- else if (source == grpsFromSelection)\r
- {\r
- makeGrpsFromSelection_actionPerformed();\r
- }\r
- else if (source == deleteGroups)\r
- {\r
- deleteGroups_actionPerformed();\r
- }\r
- else if (source == selectAllSequenceMenuItem)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed();\r
- }\r
- else if (source == deselectAllSequenceMenuItem)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed();\r
- }\r
- else if (source == invertSequenceMenuItem)\r
- {\r
- invertSequenceMenuItem_actionPerformed();\r
- }\r
- else if (source == invertColSel)\r
- {\r
- viewport.invertColumnSelection();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == remove2LeftMenuItem)\r
- {\r
- trimAlignment(true);\r
- }\r
- else if (source == remove2RightMenuItem)\r
- {\r
- trimAlignment(false);\r
- }\r
- else if (source == removeGappedColumnMenuItem)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed();\r
- }\r
- else if (source == removeAllGapsMenuItem)\r
- {\r
- removeAllGapsMenuItem_actionPerformed();\r
- }\r
- else if (source == findMenuItem)\r
- {\r
- findMenuItem_actionPerformed();\r
- }\r
- else if (source == font)\r
- {\r
- new FontChooser(alignPanel);\r
- }\r
- else if (source == newView)\r
- {\r
- newView(null);\r
- }\r
- else if (source == showColumns)\r
- {\r
- viewport.showAllHiddenColumns();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == showSeqs)\r
- {\r
- viewport.showAllHiddenSeqs();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == hideColumns)\r
- {\r
- viewport.hideSelectedColumns();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == hideSequences\r
- && viewport.getSelectionGroup() != null)\r
- {\r
- viewport.hideAllSelectedSeqs();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == hideAllButSelection)\r
- {\r
- toggleHiddenRegions(false, false);\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == hideAllSelection)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- viewport.expandColSelection(sg, false);\r
- viewport.hideAllSelectedSeqs();\r
- viewport.hideSelectedColumns();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == showAllHidden)\r
- {\r
- viewport.showAllHiddenColumns();\r
- viewport.showAllHiddenSeqs();\r
- alignPanel.paintAlignment(true);\r
- }\r
- else if (source == showGroupConsensus)\r
- {\r
- showGroupConsensus_actionPerformed();\r
- }\r
- else if (source == showGroupConservation)\r
- {\r
- showGroupConservation_actionPerformed();\r
- }\r
- else if (source == showSequenceLogo)\r
- {\r
- showSequenceLogo_actionPerformed();\r
- }\r
- else if (source == normSequenceLogo)\r
- {\r
- normSequenceLogo_actionPerformed();\r
- }\r
- else if (source == showConsensusHistogram)\r
- {\r
- showConsensusHistogram_actionPerformed();\r
- }\r
- else if (source == applyAutoAnnotationSettings)\r
- {\r
- applyAutoAnnotationSettings_actionPerformed();\r
- }\r
- else if (source == featureSettings)\r
- {\r
- new FeatureSettings(alignPanel);\r
- }\r
- else if (source == alProperties)\r
- {\r
- StringBuffer contents = new jalview.io.AlignmentProperties(\r
- viewport.getAlignment()).formatAsString();\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
- cap.setText(contents.toString());\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "\r
- + getTitle(), 400, 250);\r
- }\r
- else if (source == overviewMenuItem)\r
- {\r
- overviewMenuItem_actionPerformed();\r
- }\r
- else if (source == noColourmenuItem)\r
- {\r
- changeColour(null);\r
- }\r
- else if (source == clustalColour)\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));\r
- }\r
- else if (source == zappoColour)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
- else if (source == taylorColour)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
- else if (source == hydrophobicityColour)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
- else if (source == helixColour)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
- else if (source == strandColour)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
- else if (source == turnColour)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
- else if (source == buriedColour)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
- else if (source == nucleotideColour)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
- else if (source == purinePyrimidineColour)\r
- {\r
- changeColour(new PurinePyrimidineColourScheme());\r
- }\r
- else if (source == RNAHelixColour)\r
- {\r
- new RNAHelicesColourChooser(viewport, alignPanel);\r
- }\r
- else if (source == modifyPID)\r
- {\r
- modifyPID_actionPerformed();\r
- }\r
- else if (source == modifyConservation)\r
- {\r
- modifyConservation_actionPerformed();\r
- }\r
- else if (source == userDefinedColour)\r
- {\r
- new UserDefinedColours(alignPanel, null);\r
- }\r
- else if (source == PIDColour)\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
- else if (source == BLOSUM62Colour)\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
- }\r
- else if (source == tcoffeeColour) {\r
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
- }\r
- else if (source == annotationColour)\r
- {\r
- new AnnotationColourChooser(viewport, alignPanel);\r
- }\r
- else if (source == sortPairwiseMenuItem)\r
- {\r
- sortPairwiseMenuItem_actionPerformed();\r
- }\r
- else if (source == sortIDMenuItem)\r
- {\r
- sortIDMenuItem_actionPerformed();\r
- }\r
- else if (source == sortLengthMenuItem)\r
- {\r
- sortLengthMenuItem_actionPerformed();\r
- }\r
- else if (source == sortGroupMenuItem)\r
- {\r
- sortGroupMenuItem_actionPerformed();\r
- }\r
- else if (source == removeRedundancyMenuItem)\r
- {\r
- removeRedundancyMenuItem_actionPerformed();\r
- }\r
- else if (source == pairwiseAlignmentMenuItem)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed();\r
- }\r
- else if (source == PCAMenuItem)\r
- {\r
- PCAMenuItem_actionPerformed();\r
- }\r
- else if (source == averageDistanceTreeMenuItem)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed();\r
- }\r
- else if (source == neighbourTreeMenuItem)\r
- {\r
- neighbourTreeMenuItem_actionPerformed();\r
- }\r
- else if (source == njTreeBlosumMenuItem)\r
- {\r
- njTreeBlosumMenuItem_actionPerformed();\r
- }\r
- else if (source == avDistanceTreeBlosumMenuItem)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed();\r
- }\r
- else if (source == documentation)\r
- {\r
- documentation_actionPerformed();\r
- }\r
- else if (source == about)\r
- {\r
- about_actionPerformed();\r
- }\r
-\r
- }\r
-\r
- public void inputText_actionPerformed()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Alignment output - " + e.getActionCommand(), 600, 500);\r
- cap.setText(new AppletFormatAdapter().formatSequences(\r
- e.getActionCommand(), viewport.getAlignment(),\r
- viewport.showJVSuffix));\r
- }\r
-\r
- public void loadAnnotations()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- cap.setText("Paste your features / annotations / T-coffee score file here.");\r
- cap.setAnnotationImport();\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
-\r
- }\r
-\r
- public String outputAnnotations(boolean displayTextbox)\r
- {\r
- String annotation = new AnnotationFile().printAnnotations(\r
- viewport.showAnnotation ? viewport.getAlignment()\r
- .getAlignmentAnnotation() : null, viewport.getAlignment()\r
- .getGroups(),\r
- ((Alignment) viewport.getAlignment()).alignmentProperties);\r
-\r
- if (displayTextbox)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);\r
- cap.setText(annotation);\r
- }\r
-\r
- return annotation;\r
- }\r
-\r
- private Hashtable getDisplayedFeatureCols()\r
- {\r
- if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)\r
- {\r
- FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
- Hashtable fcols = new Hashtable();\r
- Enumeration en = viewport.featuresDisplayed.keys();\r
- while (en.hasMoreElements())\r
- {\r
- Object col = en.nextElement();\r
- fcols.put(col, fr.featureColours.get(col));\r
- }\r
- return fcols;\r
- }\r
- return null;\r
- }\r
-\r
- public String outputFeatures(boolean displayTextbox, String format)\r
- {\r
- String features;\r
- if (format.equalsIgnoreCase("Jalview"))\r
- {\r
- features = new FeaturesFile().printJalviewFormat(\r
- viewport.getAlignment().getSequencesArray(),\r
- getDisplayedFeatureCols());\r
- }\r
- else\r
- {\r
- features = new FeaturesFile().printGFFFormat(\r
- viewport.getAlignment().getSequencesArray(),\r
- getDisplayedFeatureCols());\r
- }\r
-\r
- if (displayTextbox)\r
- {\r
- boolean frimport=false;\r
- if (features==null || features.equals("No Features Visible"))\r
- {\r
- features = "# No features visible - paste some and import them here.";\r
- frimport=true;\r
- }\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
- if (frimport)\r
- {\r
- cap.setAnnotationImport();\r
- }\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
- cap.setText(features);\r
- } else {\r
- if (features==null)\r
- features = "";\r
- }\r
-\r
- return features;\r
- }\r
-\r
- void launchFullApplication()\r
- {\r
- StringBuffer url = new StringBuffer(jalviewServletURL);\r
-\r
- url.append("?open="\r
- + appendProtocol(viewport.applet.getParameter("file")));\r
-\r
- if (viewport.applet.getParameter("features") != null)\r
- {\r
- url.append("&features=");\r
- url.append(appendProtocol(viewport.applet.getParameter("features")));\r
- }\r
-\r
- if (viewport.applet.getParameter("annotations") != null)\r
- {\r
- url.append("&annotations=");\r
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
- }\r
-\r
- if (viewport.applet.getParameter("jnetfile") != null)\r
- {\r
- url.append("&annotations=");\r
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
- }\r
-\r
- if (viewport.applet.getParameter("defaultColour") != null)\r
- {\r
- url.append("&colour="\r
- + removeWhiteSpace(viewport.applet\r
- .getParameter("defaultColour")));\r
- }\r
-\r
- if (viewport.applet.getParameter("userDefinedColour") != null)\r
- {\r
- url.append("&colour="\r
- + removeWhiteSpace(viewport.applet\r
- .getParameter("userDefinedColour")));\r
- }\r
- if (viewport.applet.getParameter("tree") != null)\r
- {\r
- url.append("&tree="\r
- + appendProtocol(viewport.applet.getParameter("tree")));\r
- }\r
- if (viewport.applet.getParameter("treeFile") != null)\r
- {\r
- url.append("&tree="\r
- + appendProtocol(viewport.applet.getParameter("treeFile")));\r
- }\r
-\r
- showURL(url.toString(), "FULL_APP");\r
- }\r
-\r
- String removeWhiteSpace(String colour)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int i = 0; i < colour.length(); i++)\r
- {\r
- if (Character.isWhitespace(colour.charAt(i)))\r
- {\r
- sb.append("%20");\r
- }\r
- else\r
- {\r
- sb.append(colour.charAt(i));\r
- }\r
- }\r
-\r
- return sb.toString();\r
- }\r
-\r
- String appendProtocol(String url)\r
- {\r
- try\r
- {\r
- new URL(url);\r
- url = URLEncoder.encode(url);\r
- }\r
- /*\r
- * When we finally deprecate 1.1 compatibility, we can start to use\r
- * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch\r
- * (UnsupportedEncodingException ex) { System.err.println("WARNING -\r
- * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);\r
- * ex.printStackTrace(); }\r
- */\r
- catch (java.net.MalformedURLException ex)\r
- {\r
- url = viewport.applet.getCodeBase() + url;\r
- }\r
- return url;\r
- }\r
-\r
- public void closeMenuItem_actionPerformed()\r
- {\r
- PaintRefresher.RemoveComponent(alignPanel);\r
- if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)\r
- {\r
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
- }\r
- if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {\r
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
- }\r
-\r
- if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
- {\r
- System.exit(0);\r
- } else {\r
- }\r
- viewport = null;\r
- alignPanel = null;\r
- this.dispose();\r
- }\r
-\r
- /**\r
- * TODO: JAL-1104\r
- */\r
- void updateEditMenuBar()\r
- {\r
-\r
- if (viewport.historyList.size() > 0)\r
- {\r
- undoMenuItem.setEnabled(true);\r
- CommandI command = (CommandI) viewport.historyList.peek();\r
- undoMenuItem.setLabel("Undo " + command.getDescription());\r
- }\r
- else\r
- {\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- }\r
-\r
- if (viewport.redoList.size() > 0)\r
- {\r
- redoMenuItem.setEnabled(true);\r
-\r
- CommandI command = (CommandI) viewport.redoList.peek();\r
- redoMenuItem.setLabel("Redo " + command.getDescription());\r
- }\r
- else\r
- {\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- }\r
- }\r
-\r
- /**\r
- * TODO: JAL-1104\r
- */\r
- public void addHistoryItem(CommandI command)\r
- {\r
- if (command.getSize() > 0)\r
- {\r
- viewport.historyList.push(command);\r
- viewport.redoList.removeAllElements();\r
- updateEditMenuBar();\r
- viewport.updateHiddenColumns();\r
- }\r
- }\r
-\r
- /**\r
- * TODO: JAL-1104\r
- * DOCUMENT ME!\r
- *\r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void undoMenuItem_actionPerformed()\r
- {\r
- if (viewport.historyList.size() < 1)\r
- {\r
- return;\r
- }\r
-\r
- CommandI command = (CommandI) viewport.historyList.pop();\r
- viewport.redoList.push(command);\r
- command.undoCommand(null);\r
-\r
- AlignViewport originalSource = getOriginatingSource(command);\r
- // JBPNote Test\r
- if (originalSource!=viewport) {\r
- System.err.println("Warning: Viewport object mismatch whilst undoing");\r
- }\r
- originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;\r
- updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
- }\r
-\r
- /**\r
- * TODO: JAL-1104\r
- * DOCUMENT ME!\r
- *\r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- protected void redoMenuItem_actionPerformed()\r
- {\r
- if (viewport.redoList.size() < 1)\r
- {\r
- return;\r
- }\r
-\r
- CommandI command = (CommandI) viewport.redoList.pop();\r
- viewport.historyList.push(command);\r
- command.doCommand(null);\r
-\r
- AlignViewport originalSource = getOriginatingSource(command);\r
- // JBPNote Test\r
- if (originalSource!=viewport) {\r
- System.err.println("Warning: Viewport object mismatch whilst re-doing");\r
- }\r
- originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;\r
-\r
- updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
- }\r
-\r
- AlignViewport getOriginatingSource(CommandI command)\r
- {\r
- AlignViewport originalSource = null;\r
- // For sequence removal and addition, we need to fire\r
- // the property change event FROM the viewport where the\r
- // original alignment was altered\r
- AlignmentI al = null;\r
- if (command instanceof EditCommand)\r
- {\r
- EditCommand editCommand = (EditCommand) command;\r
- al = editCommand.getAlignment();\r
- Vector comps = (Vector) PaintRefresher.components.get(viewport\r
- .getSequenceSetId());\r
- for (int i = 0; i < comps.size(); i++)\r
- {\r
- if (comps.elementAt(i) instanceof AlignmentPanel)\r
- {\r
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())\r
- {\r
- originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
- break;\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (originalSource == null)\r
- {\r
- // The original view is closed, we must validate\r
- // the current view against the closed view first\r
- if (al != null)\r
- {\r
- PaintRefresher.validateSequences(al, viewport.getAlignment());\r
- }\r
-\r
- originalSource = viewport;\r
- }\r
-\r
- return originalSource;\r
- }\r
-\r
- public void moveSelectedSequences(boolean up)\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
- viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- synchronized void slideSequences(boolean right, int size)\r
- {\r
- List<SequenceI>sg = new Vector<SequenceI>();\r
- if (viewport.cursorMode)\r
- {\r
- sg.add(viewport.getAlignment()\r
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
- }\r
- else if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() != viewport.getAlignment()\r
- .getHeight())\r
- {\r
- sg = viewport.getSelectionGroup().getSequences(\r
- viewport.getHiddenRepSequences());\r
- }\r
-\r
- if (sg.size() < 1)\r
- {\r
- return;\r
- }\r
-\r
- Vector<SequenceI> invertGroup = new Vector();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))\r
- invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));\r
- }\r
-\r
- SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
-\r
- SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);\r
- for (int i = 0; i < invertGroup.size(); i++)\r
- seqs2[i] = invertGroup.elementAt(i);\r
-\r
- SlideSequencesCommand ssc;\r
- if (right)\r
- ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
- size, viewport.getGapCharacter());\r
- else\r
- ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
- size, viewport.getGapCharacter());\r
-\r
- int groupAdjustment = 0;\r
- if (ssc.getGapsInsertedBegin() && right)\r
- {\r
- if (viewport.cursorMode)\r
- alignPanel.seqPanel.moveCursor(size, 0);\r
- else\r
- groupAdjustment = size;\r
- }\r
- else if (!ssc.getGapsInsertedBegin() && !right)\r
- {\r
- if (viewport.cursorMode)\r
- alignPanel.seqPanel.moveCursor(-size, 0);\r
- else\r
- groupAdjustment = -size;\r
- }\r
-\r
- if (groupAdjustment != 0)\r
- {\r
- viewport.getSelectionGroup().setStartRes(\r
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
- viewport.getSelectionGroup().setEndRes(\r
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
- }\r
-\r
- boolean appendHistoryItem = false;\r
- if (viewport.historyList != null && viewport.historyList.size() > 0\r
- && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
- {\r
- appendHistoryItem = ssc\r
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
- .peek());\r
- }\r
-\r
- if (!appendHistoryItem)\r
- addHistoryItem(ssc);\r
-\r
- repaint();\r
- }\r
-\r
- static StringBuffer copiedSequences;\r
-\r
- static Vector copiedHiddenColumns;\r
-\r
- protected void copy_actionPerformed()\r
- {\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- copiedSequences = new StringBuffer();\r
- Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
- }\r
-\r
- int index = 0, startRes, endRes;\r
- char ch;\r
-\r
- if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)\r
- {\r
- copiedHiddenColumns = new Vector();\r
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
- .size(); i++)\r
- {\r
- int[] region = (int[]) viewport.getColumnSelection()\r
- .getHiddenColumns().elementAt(i);\r
-\r
- copiedHiddenColumns.addElement(new int[]\r
- { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
- }\r
- }\r
- else\r
- {\r
- copiedHiddenColumns = null;\r
- }\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
- }\r
-\r
- // FIND START RES\r
- // Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
-\r
- // FIND END RES\r
- // Need to find the residue preceeding index if gap\r
- endRes = 0;\r
-\r
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
- {\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap((ch)))\r
- {\r
- endRes++;\r
- }\r
- }\r
-\r
- if (endRes > 0)\r
- {\r
- endRes += seq.getStart() - 1;\r
- }\r
-\r
- copiedSequences.append(seq.getName()\r
- + "\t"\r
- + startRes\r
- + "\t"\r
- + endRes\r
- + "\t"\r
- + seq.getSequenceAsString(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
- }\r
-\r
- }\r
-\r
- protected void pasteNew_actionPerformed()\r
- {\r
- paste(true);\r
- }\r
-\r
- protected void pasteThis_actionPerformed()\r
- {\r
- paste(false);\r
- }\r
-\r
- void paste(boolean newAlignment)\r
- {\r
- try\r
- {\r
-\r
- if (copiedSequences == null)\r
- {\r
- return;\r
- }\r
-\r
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
- Vector seqs = new Vector();\r
- while (st.hasMoreElements())\r
- {\r
- String name = st.nextToken();\r
- int start = Integer.parseInt(st.nextToken());\r
- int end = Integer.parseInt(st.nextToken());\r
- seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
- }\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- if (newAlignment)\r
- {\r
- String newtitle = new String("Copied sequences");\r
- if (getTitle().startsWith("Copied sequences"))\r
- {\r
- newtitle = getTitle();\r
- }\r
- else\r
- {\r
- newtitle = newtitle.concat("- from " + getTitle());\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
- viewport.applet, newtitle, false);\r
- if (copiedHiddenColumns != null)\r
- {\r
- for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
- {\r
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
- af.viewport.hideColumns(region[0], region[1]);\r
- }\r
- }\r
-\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
- DEFAULT_HEIGHT);\r
- }\r
- else\r
- {\r
- addSequences(newSeqs);\r
- }\r
-\r
- } catch (Exception ex)\r
- {\r
- } // could be anything being pasted in here\r
-\r
- }\r
-\r
- void addSequences(SequenceI[] seqs)\r
- {\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- viewport.getAlignment().addSequence(seqs[i]);\r
- }\r
-\r
- // !newAlignment\r
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
- seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));\r
-\r
- viewport.setEndSeq(viewport.getAlignment().getHeight());\r
- viewport.getAlignment().getWidth();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
-\r
- }\r
-\r
- protected void cut_actionPerformed()\r
- {\r
- copy_actionPerformed();\r
- delete_actionPerformed();\r
- }\r
-\r
- protected void delete_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- Vector seqs = new Vector();\r
- SequenceI seq;\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- seq = sg.getSequenceAt(i);\r
- seqs.addElement(seq);\r
- }\r
-\r
- // If the cut affects all sequences, remove highlighted columns\r
- if (sg.getSize() == viewport.getAlignment().getHeight())\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\r
-\r
- SequenceI[] cut = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- cut[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- /*\r
- * //ADD HISTORY ITEM\r
- */\r
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
- viewport.getAlignment()));\r
-\r
- viewport.setSelectionGroup(null);\r
- viewport.getAlignment().deleteGroup(sg);\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
- .getSequences());\r
-\r
- if (viewport.getAlignment().getHeight() < 1)\r
- {\r
- this.setVisible(false);\r
- }\r
- viewport.sendSelection();\r
- }\r
-\r
- /**\r
- * group consensus toggled\r
- *\r
- */\r
- protected void showGroupConsensus_actionPerformed()\r
- {\r
- viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
-\r
- }\r
-\r
- /**\r
- * group conservation toggled.\r
- */\r
- protected void showGroupConservation_actionPerformed()\r
- {\r
- viewport.setShowGroupConservation(showGroupConservation.getState());\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- *\r
- * @see\r
- * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
- * .event.ActionEvent)\r
- */\r
- protected void showConsensusHistogram_actionPerformed()\r
- {\r
- viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
- }\r
- /*\r
- * (non-Javadoc)\r
- *\r
- * @see\r
- * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
- * .event.ActionEvent)\r
- */\r
- protected void showSequenceLogo_actionPerformed()\r
- {\r
- viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
- }\r
- protected void normSequenceLogo_actionPerformed()\r
- {\r
- showSequenceLogo.setState(true);\r
- viewport.setShowSequenceLogo(true);\r
- viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
- }\r
-\r
- protected void applyAutoAnnotationSettings_actionPerformed()\r
- {\r
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
- }\r
-\r
- protected void makeGrpsFromSelection_actionPerformed()\r
- {\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
- viewport.getSequenceSelection(),\r
- viewport.getAlignmentView(true).getSequenceStrings(\r
- viewport.getGapCharacter()),\r
- viewport.getAlignment().getGroups());\r
- viewport.getAlignment().deleteAllGroups();\r
- viewport.sequenceColours = null;\r
- viewport.setSelectionGroup(null);\r
- // set view properties for each group\r
- for (int g = 0; g < gps.length; g++)\r
- {\r
- // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
- viewport.getAlignment().addGroup(gps[g]);\r
- Color col = new Color((int) (Math.random() * 255),\r
- (int) (Math.random() * 255), (int) (Math.random() * 255));\r
- col = col.brighter();\r
- for (SequenceI sq : gps[g].getSequences(null))\r
- viewport.setSequenceColour(\r
- sq, col)\r
- ;\r
- }\r
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
- alignPanel.updateAnnotation();\r
- alignPanel.paintAlignment(true);\r
- }\r
- }\r
-\r
- protected void deleteGroups_actionPerformed()\r
- {\r
- viewport.getAlignment().deleteAllGroups();\r
- viewport.sequenceColours = null;\r
- viewport.setSelectionGroup(null);\r
-\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public void selectAllSequenceMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
- sg.setEndRes(viewport.getAlignment().getWidth() - 1);\r
- viewport.setSelectionGroup(sg);\r
- alignPanel.paintAlignment(true);\r
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
- viewport.sendSelection();\r
- }\r
-\r
- public void deselectAllSequenceMenuItem_actionPerformed()\r
- {\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.keyboardNo1 = null;\r
- alignPanel.seqPanel.keyboardNo2 = null;\r
- }\r
- viewport.setSelectionGroup(null);\r
- viewport.getColumnSelection().clear();\r
- viewport.setSelectionGroup(null);\r
- alignPanel.idPanel.idCanvas.searchResults = null;\r
- alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
- alignPanel.paintAlignment(true);\r
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
- viewport.sendSelection();\r
- }\r
-\r
- public void invertSequenceMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
- viewport.sendSelection();\r
- }\r
-\r
- public void invertColSel_actionPerformed()\r
- {\r
- viewport.invertColumnSelection();\r
- alignPanel.paintAlignment(true);\r
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
- viewport.sendSelection();\r
- }\r
-\r
- void trimAlignment(boolean trimLeft)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- int column;\r
-\r
- if (colSel.size() > 0)\r
- {\r
- if (trimLeft)\r
- {\r
- column = colSel.getMin();\r
- }\r
- else\r
- {\r
- column = colSel.getMax();\r
- }\r
-\r
- SequenceI[] seqs;\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
- viewport.getHiddenRepSequences());\r
- }\r
- else\r
- {\r
- seqs = viewport.getAlignment().getSequencesArray();\r
- }\r
-\r
- TrimRegionCommand trimRegion;\r
- if (trimLeft)\r
- {\r
- trimRegion = new TrimRegionCommand("Remove Left",\r
- TrimRegionCommand.TRIM_LEFT, seqs, column,\r
- viewport.getAlignment(), viewport.getColumnSelection(),\r
- viewport.getSelectionGroup());\r
- viewport.setStartRes(0);\r
- }\r
- else\r
- {\r
- trimRegion = new TrimRegionCommand("Remove Right",\r
- TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
- viewport.getAlignment(), viewport.getColumnSelection(),\r
- viewport.getSelectionGroup());\r
- }\r
-\r
- statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
-\r
- addHistoryItem(trimRegion);\r
-\r
-\r
-\r
- for (SequenceGroup sg:viewport.getAlignment().getGroups())\r
- {\r
- if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
- || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
- {\r
- viewport.getAlignment().deleteGroup(sg);\r
- }\r
- }\r
-\r
- viewport.firePropertyChange("alignment", null, viewport\r
- .getAlignment().getSequences());\r
- }\r
- }\r
-\r
- public void removeGappedColumnMenuItem_actionPerformed()\r
- {\r
- int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
-\r
- SequenceI[] seqs;\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
- viewport.getHiddenRepSequences());\r
- start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
- }\r
- else\r
- {\r
- seqs = viewport.getAlignment().getSequencesArray();\r
- }\r
-\r
- RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
- "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());\r
-\r
- addHistoryItem(removeGapCols);\r
-\r
- statusBar.setText("Removed " + removeGapCols.getSize()\r
- + " empty columns.");\r
-\r
- // This is to maintain viewport position on first residue\r
- // of first sequence\r
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
- // ShiftList shifts;\r
- // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
- // edit.alColumnChanges=shifts.getInverse();\r
- // if (viewport.hasHiddenColumns)\r
- // viewport.getColumnSelection().compensateForEdits(shifts);\r
- viewport.setStartRes(seq.findIndex(startRes) - 1);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
- .getSequences());\r
-\r
- }\r
-\r
- public void removeAllGapsMenuItem_actionPerformed()\r
- {\r
- int start = 0, end = viewport.getAlignment().getWidth() - 1;\r
-\r
- SequenceI[] seqs;\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
- viewport.getHiddenRepSequences());\r
- start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
- }\r
- else\r
- {\r
- seqs = viewport.getAlignment().getSequencesArray();\r
- }\r
-\r
- // This is to maintain viewport position on first residue\r
- // of first sequence\r
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
-\r
- addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
- viewport.getAlignment()));\r
-\r
- viewport.setStartRes(seq.findIndex(startRes) - 1);\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
- .getSequences());\r
-\r
- }\r
-\r
- public void findMenuItem_actionPerformed()\r
- {\r
- new Finder(alignPanel);\r
- }\r
-\r
- /**\r
- * create a new view derived from the current view\r
- *\r
- * @param viewtitle\r
- * @return frame for the new view\r
- */\r
- public AlignFrame newView(String viewtitle)\r
- {\r
- AlignmentI newal;\r
- if (viewport.hasHiddenRows())\r
- {\r
- newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
- .getFullAlignment().getSequencesArray());\r
- }\r
- else\r
- {\r
- newal = new Alignment(viewport.getAlignment().getSequencesArray());\r
- }\r
-\r
- if (viewport.getAlignment().getAlignmentAnnotation() != null)\r
- {\r
- for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)\r
- {\r
- if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)\r
- {\r
- newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);\r
- }\r
- }\r
- }\r
-\r
- AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
-\r
- newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());\r
- PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
- PaintRefresher.Register(newaf.alignPanel,\r
- newaf.alignPanel.av.getSequenceSetId());\r
-\r
- PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
- newaf.alignPanel.av.getSequenceSetId());\r
- PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
- newaf.alignPanel.av.getSequenceSetId());\r
-\r
- Vector comps = (Vector) PaintRefresher.components.get(viewport\r
- .getSequenceSetId());\r
- int viewSize = -1;\r
- for (int i = 0; i < comps.size(); i++)\r
- {\r
- if (comps.elementAt(i) instanceof AlignmentPanel)\r
- {\r
- viewSize++;\r
- }\r
- }\r
-\r
- String title = new String(this.getTitle());\r
- if (viewtitle != null)\r
- {\r
- title = viewtitle + " ( " + title + ")";\r
- }\r
- else\r
- {\r
- if (title.indexOf("(View") > -1)\r
- {\r
- title = title.substring(0, title.indexOf("(View"));\r
- }\r
- title += "(View " + viewSize + ")";\r
- }\r
-\r
- newaf.setTitle(title.toString());\r
-\r
- newaf.viewport.historyList = viewport.historyList;\r
- newaf.viewport.redoList = viewport.redoList;\r
- return newaf;\r
- }\r
-\r
- /**\r
- *\r
- * @return list of feature groups on the view\r
- */\r
- public String[] getFeatureGroups()\r
- {\r
- FeatureRenderer fr = null;\r
- if (alignPanel != null\r
- && (fr = alignPanel.getFeatureRenderer()) != null)\r
- {\r
- return fr.getGroups();\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * get sequence feature groups that are hidden or shown\r
- *\r
- * @param visible\r
- * true is visible\r
- * @return list\r
- */\r
- public String[] getFeatureGroupsOfState(boolean visible)\r
- {\r
- FeatureRenderer fr = null;\r
- if (alignPanel != null\r
- && (fr = alignPanel.getFeatureRenderer()) != null)\r
- {\r
- return fr.getGroups(visible);\r
- }\r
- return null;\r
- }\r
-\r
- /**\r
- * Change the display state for the given feature groups\r
- *\r
- * @param groups\r
- * list of group strings\r
- * @param state\r
- * visible or invisible\r
- */\r
- public void setFeatureGroupState(String[] groups, boolean state)\r
- {\r
- FeatureRenderer fr = null;\r
- this.sequenceFeatures.setState(true);\r
- viewport.showSequenceFeatures(true);\r
- if (alignPanel != null\r
- && (fr = alignPanel.getFeatureRenderer()) != null)\r
- {\r
- fr.setGroupState(groups, state);\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- alignPanel.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- }\r
-\r
- public void seqLimits_itemStateChanged()\r
- {\r
- viewport.setShowJVSuffix(seqLimits.getState());\r
- alignPanel.fontChanged();\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed()\r
- {\r
- viewport.setColourText(colourTextMenuItem.getState());\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- protected void displayNonconservedMenuItem_actionPerformed()\r
- {\r
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed()\r
- {\r
- viewport.setWrapAlignment(wrapMenuItem.getState());\r
- alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
- scaleAbove.setEnabled(wrapMenuItem.getState());\r
- scaleLeft.setEnabled(wrapMenuItem.getState());\r
- scaleRight.setEnabled(wrapMenuItem.getState());\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public void overviewMenuItem_actionPerformed()\r
- {\r
- if (alignPanel.overviewPanel != null)\r
- {\r
- return;\r
- }\r
-\r
- Frame frame = new Frame();\r
- OverviewPanel overview = new OverviewPanel(alignPanel);\r
- frame.add(overview);\r
- // +50 must allow for applet frame window\r
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.getPreferredSize().width,\r
- overview.getPreferredSize().height + 50);\r
-\r
- frame.pack();\r
- final AlignmentPanel ap=alignPanel;\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- @Override\r
- public void windowClosing(WindowEvent e)\r
- {\r
- if (ap!=null) {\r
- ap.setOverviewPanel(null);\r
- }\r
- };\r
- });\r
-\r
- alignPanel.setOverviewPanel(overview);\r
-\r
- }\r
-\r
- void changeColour(ColourSchemeI cs)\r
- {\r
- int threshold = 0;\r
-\r
- if (cs != null)\r
- {\r
- if (viewport.getAbovePIDThreshold())\r
- {\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
- "Background");\r
-\r
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-\r
- viewport.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
-\r
- Alignment al = (Alignment) viewport.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() - 1);\r
-\r
- c.calculate();\r
- c.verdict(false, viewport.getConsPercGaps());\r
-\r
- cs.setConservation(c);\r
-\r
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
- cs, "Background"));\r
-\r
- }\r
- else\r
- {\r
- cs.setConservation(null);\r
- }\r
-\r
- cs.setConsensus(viewport.getSequenceConsensusHash());\r
-\r
- }\r
- viewport.setGlobalColourScheme(cs);\r
-\r
-\r
- if (alignPanel.getOverviewPanel() != null)\r
- {\r
- alignPanel.getOverviewPanel().updateOverviewImage();\r
- }\r
-\r
- jalview.structure.StructureSelectionManager\r
- .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(\r
- alignPanel);\r
-\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- protected void modifyPID_actionPerformed()\r
- {\r
- if (viewport.getAbovePIDThreshold()\r
- && viewport.getGlobalColourScheme() != null)\r
- {\r
- SliderPanel.setPIDSliderSource(alignPanel,\r
- viewport.getGlobalColourScheme(), "Background");\r
- SliderPanel.showPIDSlider();\r
- }\r
- }\r
-\r
- protected void modifyConservation_actionPerformed()\r
- {\r
- if (viewport.getConservationSelected()\r
- && viewport.getGlobalColourScheme() != null)\r
- {\r
- SliderPanel.setConservationSlider(alignPanel,\r
- viewport.getGlobalColourScheme(), "Background");\r
- SliderPanel.showConservationSlider();\r
- }\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- viewport.setConservationSelected(conservationMenuItem.getState());\r
-\r
- viewport.setAbovePIDThreshold(false);\r
- abovePIDThreshold.setState(false);\r
-\r
- changeColour(viewport.getGlobalColourScheme());\r
-\r
- modifyConservation_actionPerformed();\r
- }\r
-\r
- public void abovePIDThreshold_actionPerformed()\r
- {\r
- viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
-\r
- conservationMenuItem.setState(false);\r
- viewport.setConservationSelected(false);\r
-\r
- changeColour(viewport.getGlobalColourScheme());\r
-\r
- modifyPID_actionPerformed();\r
- }\r
-\r
- public void sortPairwiseMenuItem_actionPerformed()\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
- .getAlignment().getSequenceAt(0), null);\r
-\r
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
- viewport.getAlignment()));\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public void sortIDMenuItem_actionPerformed()\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter.sortByID(viewport.getAlignment());\r
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public void sortLengthMenuItem_actionPerformed()\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter.sortByLength(viewport.getAlignment());\r
- addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
- viewport.getAlignment()));\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- public void sortGroupMenuItem_actionPerformed()\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
- viewport.getAlignment()));\r
- alignPanel.paintAlignment(true);\r
-\r
- }\r
-\r
- public void removeRedundancyMenuItem_actionPerformed()\r
- {\r
- new RedundancyPanel(alignPanel);\r
- }\r
-\r
- public void pairwiseAlignmentMenuItem_actionPerformed()\r
- {\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() > 1)\r
- {\r
- Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(alignPanel));\r
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,\r
- 500);\r
- }\r
- }\r
-\r
- public void PCAMenuItem_actionPerformed()\r
- {\r
- // are the sequences aligned?\r
- if (!viewport.getAlignment().isAligned(false))\r
- {\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
- }\r
- }\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- if ((viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() < 4 && viewport\r
- .getSelectionGroup().getSize() > 0)\r
- || viewport.getAlignment().getHeight() < 4)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- new PCAPanel(viewport);\r
- } catch (java.lang.OutOfMemoryError ex)\r
- {\r
- }\r
-\r
- }\r
-\r
- public void averageDistanceTreeMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("AV", "PID", "Average distance tree using PID");\r
- }\r
-\r
- public void neighbourTreeMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
- }\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed()\r
- {\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
- }\r
-\r
- void NewTreePanel(String type, String pwType, String title)\r
- {\r
- // are the sequences aligned?\r
- if (!viewport.getAlignment().isAligned(false))\r
- {\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
- }\r
- }\r
- alignPanel.paintAlignment(true);\r
-\r
- }\r
-\r
- if ((viewport.getSelectionGroup() != null && viewport\r
- .getSelectionGroup().getSize() > 1)\r
- || (viewport.getAlignment()\r
- .getHeight() > 1))\r
- {\r
- final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
-\r
- addTreeMenuItem(tp, title);\r
-\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
- }\r
- }\r
-\r
- void loadTree_actionPerformed()\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- cap.setText("Paste your Newick tree file here.");\r
- cap.setTreeImport();\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
- }\r
-\r
- public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
- {\r
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
- }\r
-\r
- /**\r
- * sort the alignment using the given treePanel\r
- *\r
- * @param treePanel\r
- * tree used to sort view\r
- * @param title\r
- * string used for undo event name\r
- */\r
- public void sortByTree(TreePanel treePanel, String title)\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter\r
- .sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- // HistoryItem.SORT));\r
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
- viewport.getAlignment()));\r
- alignPanel.paintAlignment(true);\r
- }\r
-\r
- /**\r
- * Do any automatic reordering of the alignment and add the necessary bits to\r
- * the menu structure for the new tree\r
- *\r
- * @param treePanel\r
- * @param title\r
- */\r
- protected void addTreeMenuItem(final TreePanel treePanel,\r
- final String title)\r
- {\r
- final MenuItem item = new MenuItem(title);\r
- sortByTreeMenu.add(item);\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- @Override\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- sortByTree(treePanel, title); // treePanel.getTitle());\r
- }\r
- });\r
-\r
- treePanel.addWindowListener(new WindowAdapter()\r
- {\r
- @Override\r
- public void windowOpened(WindowEvent e)\r
- {\r
- if (viewport.sortByTree)\r
- {\r
- sortByTree(treePanel, title);\r
- }\r
- super.windowOpened(e);\r
- }\r
-\r
- @Override\r
- public void windowClosing(WindowEvent e)\r
- {\r
- sortByTreeMenu.remove(item);\r
- };\r
- });\r
- }\r
- public boolean sortBy(AlignmentOrder alorder, String undoname)\r
- {\r
- SequenceI[] oldOrder = viewport.getAlignment()\r
- .getSequencesArray();\r
- if (viewport.applet.debug)\r
- {\r
- System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
- }\r
- AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
- if (undoname!=null)\r
- {\r
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));\r
- }\r
- alignPanel.paintAlignment(true);\r
- return true;\r
- }\r
-\r
- protected void documentation_actionPerformed()\r
- {\r
- alignPanel.av.applet.openJalviewHelpUrl();\r
- }\r
-\r
- protected void about_actionPerformed()\r
- {\r
-\r
- class AboutPanel extends Canvas\r
- {\r
- String version;\r
-\r
- String builddate;\r
-\r
- public AboutPanel(String version, String builddate)\r
- {\r
- this.version = version;\r
- this.builddate = builddate;\r
- }\r
-\r
- @Override\r
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- FontMetrics fm = g.getFontMetrics();\r
- int fh = fm.getHeight();\r
- int y = 5, x = 7;\r
- g.setColor(Color.black);\r
- // TODO: update this text for each release or centrally store it for\r
- // lite and application\r
- g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("JalviewLite - Release " + version, x, y += fh);\r
- g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
- g.drawString("Build date: " + builddate, x, y += fh);\r
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- g.drawString(\r
- "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
- x, y += fh * 1.5);\r
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
- g.drawString(\r
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
- x, y += fh);\r
- g.drawString(\r
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
- x, y += fh);\r
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);\r
- g.drawString(\r
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
- x, y += fh);\r
- g.drawString(\r
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
- x, y += fh);\r
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
- x, y += fh);\r
- }\r
- }\r
-\r
- Frame frame = new Frame();\r
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
- .getBuildDate()));\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
-\r
- }\r
-\r
- public void showURL(String url, String target)\r
- {\r
- if (viewport.applet == null)\r
- {\r
- System.out.println("Not running as applet - no browser available.");\r
- }\r
- else\r
- {\r
- viewport.applet.showURL(url, target);\r
- }\r
- }\r
-\r
- // ////////////////////////////////////////////////////////////////////////////////\r
- // JBuilder Graphics here\r
-\r
- MenuBar alignFrameMenuBar = new MenuBar();\r
-\r
- Menu fileMenu = new Menu("File");\r
-\r
- MenuItem loadApplication = new MenuItem("View in Full Application");\r
-\r
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
-\r
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
-\r
- MenuItem outputFeatures = new MenuItem("Export Features ...");\r
-\r
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
-\r
- MenuItem closeMenuItem = new MenuItem("Close");\r
-\r
- Menu editMenu = new Menu("Edit");\r
-\r
- Menu viewMenu = new Menu("View");\r
-\r
- Menu colourMenu = new Menu("Colour");\r
-\r
- Menu calculateMenu = new Menu("Calculate");\r
-\r
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
-\r
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
-\r
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
-\r
- MenuItem remove2LeftMenuItem = new MenuItem();\r
-\r
- MenuItem remove2RightMenuItem = new MenuItem();\r
-\r
- MenuItem removeGappedColumnMenuItem = new MenuItem();\r
-\r
- MenuItem removeAllGapsMenuItem = new MenuItem();\r
-\r
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
-\r
- MenuItem sortPairwiseMenuItem = new MenuItem();\r
-\r
- MenuItem sortIDMenuItem = new MenuItem();\r
-\r
- MenuItem sortLengthMenuItem = new MenuItem();\r
-\r
- MenuItem sortGroupMenuItem = new MenuItem();\r
-\r
- MenuItem removeRedundancyMenuItem = new MenuItem();\r
-\r
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
-\r
- MenuItem PCAMenuItem = new MenuItem();\r
-\r
- MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
-\r
- MenuItem neighbourTreeMenuItem = new MenuItem();\r
-\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
- public Label statusBar = new Label();\r
-\r
- Menu outputTextboxMenu = new Menu();\r
-\r
- MenuItem clustalColour = new MenuItem();\r
-\r
- MenuItem zappoColour = new MenuItem();\r
-\r
- MenuItem taylorColour = new MenuItem();\r
-\r
- MenuItem hydrophobicityColour = new MenuItem();\r
-\r
- MenuItem helixColour = new MenuItem();\r
-\r
- MenuItem strandColour = new MenuItem();\r
-\r
- MenuItem turnColour = new MenuItem();\r
-\r
- MenuItem buriedColour = new MenuItem();\r
-\r
- MenuItem purinePyrimidineColour = new MenuItem();\r
- MenuItem RNAHelixColour = new MenuItem();\r
-\r
- MenuItem userDefinedColour = new MenuItem();\r
-\r
- MenuItem PIDColour = new MenuItem();\r
-\r
- MenuItem BLOSUM62Colour = new MenuItem();\r
-\r
- MenuItem tcoffeeColour = new MenuItem();\r
-\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
-\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
-\r
- CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
-\r
- MenuItem alProperties = new MenuItem("Alignment Properties...");\r
-\r
- MenuItem overviewMenuItem = new MenuItem();\r
-\r
- MenuItem undoMenuItem = new MenuItem();\r
-\r
- MenuItem redoMenuItem = new MenuItem();\r
-\r
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
-\r
- MenuItem noColourmenuItem = new MenuItem();\r
-\r
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
-\r
- MenuItem findMenuItem = new MenuItem();\r
-\r
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
-\r
- MenuItem nucleotideColour = new MenuItem();\r
-\r
- MenuItem deleteGroups = new MenuItem();\r
-\r
- MenuItem grpsFromSelection = new MenuItem();\r
-\r
- MenuItem delete = new MenuItem();\r
-\r
- MenuItem copy = new MenuItem();\r
-\r
- MenuItem cut = new MenuItem();\r
-\r
- Menu pasteMenu = new Menu();\r
-\r
- MenuItem pasteNew = new MenuItem();\r
-\r
- MenuItem pasteThis = new MenuItem();\r
-\r
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
-\r
- MenuItem font = new MenuItem();\r
-\r
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
-\r
- MenuItem modifyPID = new MenuItem();\r
-\r
- MenuItem modifyConservation = new MenuItem();\r
-\r
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
- "Autocalculate Consensus", true);\r
-\r
- CheckboxMenuItem sortByTree = new CheckboxMenuItem(\r
- "Sort Alignment With New Tree", true);\r
-\r
- Menu sortByTreeMenu = new Menu();\r
-\r
- Menu sort = new Menu();\r
-\r
- Menu calculate = new Menu();\r
-\r
- MenuItem inputText = new MenuItem();\r
-\r
- Menu helpMenu = new Menu();\r
-\r
- MenuItem documentation = new MenuItem();\r
-\r
- MenuItem about = new MenuItem();\r
-\r
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
-\r
- CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
- Menu autoAnnMenu=new Menu();\r
- CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
- CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
- CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
- CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
- CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
- CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();\r
-\r
- private void jbInit() throws Exception\r
- {\r
-\r
- setMenuBar(alignFrameMenuBar);\r
-\r
- MenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
-\r
- item = new MenuItem(\r
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- @Override\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- closeMenuItem.addActionListener(this);\r
- loadApplication.addActionListener(this);\r
-\r
- loadTree.addActionListener(this);\r
- loadAnnotations.addActionListener(this);\r
- outputFeatures.addActionListener(this);\r
- outputAnnotations.addActionListener(this);\r
- selectAllSequenceMenuItem.addActionListener(this);\r
- deselectAllSequenceMenuItem.addActionListener(this);\r
- invertSequenceMenuItem.addActionListener(this);\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(this);\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(this);\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(this);\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(this);\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(this);\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(this);\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(this);\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(this);\r
- sortLengthMenuItem.setLabel("by Length");\r
- sortLengthMenuItem.addActionListener(this);\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(this);\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(this);\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(this);\r
- PCAMenuItem.setLabel("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(this);\r
- averageDistanceTreeMenuItem\r
- .setLabel("Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(this);\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(this);\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(this);\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(this);\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(this);\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(this);\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(this);\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(this);\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(this);\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(this);\r
- purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
- purinePyrimidineColour.addActionListener(this);\r
- RNAHelixColour.setLabel("by RNA Helices");\r
- RNAHelixColour.addActionListener(this);\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(this);\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(this);\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(this);\r
- tcoffeeColour.setLabel("T-Coffee Scores");\r
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided\r
- tcoffeeColour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(this);\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(this);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(this);\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(this);\r
- displayNonconservedMenuItem.setLabel("Show nonconserved");\r
- displayNonconservedMenuItem.addItemListener(this);\r
- alProperties.addActionListener(this);\r
- overviewMenuItem.setLabel("Overview Window");\r
- overviewMenuItem.addActionListener(this);\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(this);\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(this);\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(this);\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(this);\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(this);\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(this);\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(this);\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(this);\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(this);\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(this);\r
- grpsFromSelection.setLabel("Make Groups for selection");\r
- grpsFromSelection.addActionListener(this);\r
- copy.setLabel("Copy");\r
- copy.addActionListener(this);\r
- cut.setLabel("Cut");\r
- cut.addActionListener(this);\r
- delete.setLabel("Delete");\r
- delete.addActionListener(this);\r
- pasteMenu.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(this);\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(this);\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(this);\r
- font.setLabel("Font...");\r
- font.addActionListener(this);\r
- scaleAbove.setLabel("Scale Above");\r
- scaleAbove.setState(true);\r
- scaleAbove.setEnabled(false);\r
- scaleAbove.addItemListener(this);\r
- scaleLeft.setEnabled(false);\r
- scaleLeft.setState(true);\r
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(this);\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(this);\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(this);\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(this);\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- autoCalculate.addItemListener(this);\r
- sortByTree.addItemListener(this);\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(this);\r
- centreColumnLabelFlag.setLabel("Centre column labels");\r
- centreColumnLabelFlag.addItemListener(this);\r
- followMouseOverFlag.setLabel("Automatic Scrolling");\r
- followMouseOverFlag.addItemListener(this);\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(this);\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(this);\r
- seqLimits.setState(true);\r
- seqLimits.setLabel("Show Sequence Limits");\r
- seqLimits.addItemListener(this);\r
- featureSettings.setLabel("Feature Settings...");\r
- featureSettings.addActionListener(this);\r
- sequenceFeatures.setLabel("Sequence Features");\r
- sequenceFeatures.addItemListener(this);\r
- sequenceFeatures.setState(false);\r
- annotationColour.setLabel("by Annotation...");\r
- annotationColour.addActionListener(this);\r
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
- invertColSel.setLabel("Invert Column Selection");\r
- menu1.setLabel("Show");\r
- showColumns.setLabel("All Columns ");\r
- showSeqs.setLabel("All Sequences");\r
- menu2.setLabel("Hide");\r
- hideColumns.setLabel("Selected Columns");\r
- hideSequences.setLabel("Selected Sequences");\r
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");\r
- hideAllSelection.setLabel("Selected Region");\r
- showAllHidden.setLabel("All Sequences and Columns");\r
- showGroupConsensus.setLabel("Group Consensus");\r
- showGroupConservation.setLabel("Group Conservation");\r
- showConsensusHistogram.setLabel("Show Consensus Histogram");\r
- showSequenceLogo.setLabel("Show Consensus Logo");\r
- normSequenceLogo.setLabel("Normalise Consensus Logo");\r
- applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
- applyAutoAnnotationSettings.setState(true);\r
- autoAnnMenu.setLabel("Autocalculated Annotation");\r
-\r
- invertColSel.addActionListener(this);\r
- showColumns.addActionListener(this);\r
- showSeqs.addActionListener(this);\r
- hideColumns.addActionListener(this);\r
- hideSequences.addActionListener(this);\r
- hideAllButSelection.addActionListener(this);\r
- hideAllSelection.addActionListener(this);\r
- showAllHidden.addActionListener(this);\r
- showGroupConsensus.addItemListener(this);\r
- showGroupConservation.addItemListener(this);\r
- showConsensusHistogram.addItemListener(this);\r
- showSequenceLogo.addItemListener(this);\r
- normSequenceLogo.addItemListener(this);\r
- \r
- applyAutoAnnotationSettings.addItemListener(this);\r
- formatMenu.setLabel("Format");\r
- selectMenu.setLabel("Select");\r
- newView.setLabel("New View");\r
- newView.addActionListener(this);\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(selectMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(formatMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(helpMenu);\r
-\r
- fileMenu.add(inputText);\r
- fileMenu.add(loadTree);\r
- fileMenu.add(loadAnnotations);\r
-\r
- fileMenu.addSeparator();\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.add(outputFeatures);\r
- fileMenu.add(outputAnnotations);\r
-\r
- if (jalviewServletURL != null)\r
- {\r
- fileMenu.add(loadApplication);\r
- }\r
-\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
-\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(pasteMenu);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- viewMenu.add(newView);\r
- viewMenu.addSeparator();\r
- viewMenu.add(menu1);\r
- viewMenu.add(menu2);\r
- viewMenu.addSeparator();\r
- viewMenu.add(followMouseOverFlag);\r
- viewMenu.add(annotationPanelMenuItem);\r
- autoAnnMenu.add(applyAutoAnnotationSettings);\r
- autoAnnMenu.add(showConsensusHistogram);\r
- autoAnnMenu.add(showSequenceLogo);\r
- autoAnnMenu.add(normSequenceLogo);\r
- autoAnnMenu.addSeparator();\r
- autoAnnMenu.add(showGroupConservation);\r
- autoAnnMenu.add(showGroupConsensus);\r
- viewMenu.add(autoAnnMenu);\r
- viewMenu.addSeparator();\r
- viewMenu.add(sequenceFeatures);\r
- viewMenu.add(featureSettings);\r
- viewMenu.addSeparator();\r
- viewMenu.add(alProperties);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(purinePyrimidineColour);\r
- colourMenu.add(tcoffeeColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- colourMenu.add(annotationColour);\r
- colourMenu.add(RNAHelixColour);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- calculateMenu.add(autoCalculate);\r
- calculateMenu.add(sortByTree);\r
- this.add(statusBar, BorderLayout.SOUTH);\r
- pasteMenu.add(pasteNew);\r
- pasteMenu.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortLengthMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\r
- menu1.add(showColumns);\r
- menu1.add(showSeqs);\r
- menu1.add(showAllHidden);\r
- menu2.add(hideColumns);\r
- menu2.add(hideSequences);\r
- menu2.add(hideAllSelection);\r
- menu2.add(hideAllButSelection);\r
- formatMenu.add(font);\r
- formatMenu.add(seqLimits);\r
- formatMenu.add(wrapMenuItem);\r
- formatMenu.add(scaleAbove);\r
- formatMenu.add(scaleLeft);\r
- formatMenu.add(scaleRight);\r
- formatMenu.add(viewBoxesMenuItem);\r
- formatMenu.add(viewTextMenuItem);\r
- formatMenu.add(colourTextMenuItem);\r
- formatMenu.add(displayNonconservedMenuItem);\r
- formatMenu.add(renderGapsMenuItem);\r
- formatMenu.add(centreColumnLabelFlag);\r
- selectMenu.add(findMenuItem);\r
- selectMenu.addSeparator();\r
- selectMenu.add(selectAllSequenceMenuItem);\r
- selectMenu.add(deselectAllSequenceMenuItem);\r
- selectMenu.add(invertSequenceMenuItem);\r
- selectMenu.add(invertColSel);\r
- selectMenu.add(grpsFromSelection);\r
- selectMenu.add(deleteGroups);\r
-\r
- }\r
-\r
- MenuItem featureSettings = new MenuItem();\r
-\r
- CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
-\r
- MenuItem annotationColour = new MenuItem();\r
-\r
- MenuItem invertColSel = new MenuItem();\r
-\r
- Menu menu1 = new Menu();\r
-\r
- MenuItem showColumns = new MenuItem();\r
-\r
- MenuItem showSeqs = new MenuItem();\r
-\r
- Menu menu2 = new Menu();\r
-\r
- MenuItem hideColumns = new MenuItem();\r
-\r
- MenuItem hideSequences = new MenuItem();\r
-\r
- MenuItem hideAllButSelection = new MenuItem();\r
-\r
- MenuItem hideAllSelection = new MenuItem();\r
-\r
- MenuItem showAllHidden = new MenuItem();\r
-\r
- Menu formatMenu = new Menu();\r
-\r
- Menu selectMenu = new Menu();\r
-\r
- MenuItem newView = new MenuItem();\r
-\r
- /**\r
- * Attach the alignFrame panels after embedding menus, if necessary. This used\r
- * to be called setEmbedded, but is now creates the dropdown menus in a\r
- * platform independent manner to avoid OSX/Mac menu appendage daftness.\r
- *\r
- * @param reallyEmbedded\r
- * true to attach the view to the applet area on the page rather than\r
- * in a new window\r
- */\r
- public void createAlignFrameWindow(boolean reallyEmbedded, String title)\r
- {\r
- if (reallyEmbedded)\r
- {\r
- // ////\r
- // Explicly build the embedded menu panel for the on-page applet\r
- //\r
- // view cannot be closed if its actually on the page\r
- fileMenu.remove(closeMenuItem);\r
- fileMenu.remove(3); // Remove Seperator\r
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",\r
- Font.PLAIN, 10, false); // use our own fonts.\r
- // and actually add the components to the applet area\r
- viewport.applet.setLayout(new BorderLayout());\r
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
- viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
- alignPanel.setSize(viewport.applet.getSize().width,\r
- viewport.applet.getSize().height - embeddedMenu.HEIGHT\r
- - statusBar.HEIGHT);\r
- viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
- final AlignFrame me = this;\r
- viewport.applet.addFocusListener(new FocusListener()\r
- {\r
-\r
- @Override\r
- public void focusLost(FocusEvent e)\r
- {\r
- if (me.viewport.applet.currentAlignFrame==me) {\r
- me.viewport.applet.currentAlignFrame = null;\r
- }}\r
-\r
- @Override\r
- public void focusGained(FocusEvent e)\r
- {\r
- me.viewport.applet.currentAlignFrame = me;\r
- }\r
- });\r
- viewport.applet.validate();\r
- }\r
- else\r
- {\r
- // //////\r
- // test and embed menu bar if necessary.\r
- //\r
- if (embedMenuIfNeeded(alignPanel))\r
- {\r
- // adjust for status bar height too\r
- alignPanel.setSize(getSize().width, getSize().height\r
- - statusBar.HEIGHT);\r
- }\r
- add(statusBar, BorderLayout.SOUTH);\r
- add(alignPanel, BorderLayout.CENTER);\r
- // and register with the applet so it can pass external API calls to us\r
- jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
- DEFAULT_HEIGHT);\r
- }\r
- }\r
-\r
- /**\r
- * create a new binding between structures in an existing jmol viewer instance\r
- * and an alignpanel with sequences that have existing PDBFile entries. Note,\r
- * this does not open a new Jmol window, or modify the display of the\r
- * structures in the original jmol window. Note This method doesn't work\r
- * without an additional javascript library to exchange messages between the\r
- * distinct applets. See http://issues.jalview.org/browse/JAL-621\r
- *\r
- * @param viewer\r
- * JmolViewer instance\r
- * @param sequenceIds\r
- * - sequence Ids to search for associations\r
- */\r
- public SequenceStructureBinding addStructureViewInstance(\r
- Object jmolviewer, String[] sequenceIds)\r
- {\r
- org.jmol.api.JmolViewer viewer = null;\r
- try\r
- {\r
- viewer = (org.jmol.api.JmolViewer) jmolviewer;\r
- } catch (ClassCastException ex)\r
- {\r
- System.err.println("Unsupported viewer object :"\r
- + jmolviewer.getClass());\r
- }\r
- if (viewer == null)\r
- {\r
- System.err.println("Can't use this object as a structure viewer:"\r
- + jmolviewer.getClass());\r
- return null;\r
- }\r
- SequenceI[] seqs = null;\r
- if (sequenceIds == null || sequenceIds.length == 0)\r
- {\r
- seqs = viewport.getAlignment().getSequencesArray();\r
- }\r
- else\r
- {\r
- Vector sqi = new Vector();\r
- AlignmentI al = viewport.getAlignment();\r
- for (int sid = 0; sid < sequenceIds.length; sid++)\r
- {\r
- SequenceI sq = al.findName(sequenceIds[sid]);\r
- if (sq != null)\r
- {\r
- sqi.addElement(sq);\r
- }\r
- }\r
- if (sqi.size() > 0)\r
- {\r
- seqs = new SequenceI[sqi.size()];\r
- for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)\r
- {\r
- seqs[sid] = (SequenceI) sqi.elementAt(sid);\r
- }\r
- }\r
- else\r
- {\r
- return null;\r
- }\r
- }\r
- ExtJmol jmv = null;\r
- // TODO: search for a jmv that involves viewer\r
- if (jmv == null)\r
- { // create a new viewer/jalview binding.\r
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
- }\r
- return jmv;\r
-\r
- }\r
- /**\r
- * bind a pdb file to a sequence in the current view\r
- *\r
- * @param sequenceId\r
- * - sequenceId within the dataset.\r
- * @param pdbEntryString\r
- * - the short name for the PDB file\r
- * @param pdbFile\r
- * - pdb file - either a URL or a valid PDB file.\r
- * @return true if binding was as success TODO: consider making an exception\r
- * structure for indicating when PDB parsing or sequenceId location\r
- * fails.\r
- */\r
- public boolean addPdbFile(String sequenceId, String pdbEntryString,\r
- String pdbFile)\r
- {\r
- SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);\r
- boolean needtoadd = false;\r
- if (toaddpdb != null)\r
- {\r
- Vector pdbe = toaddpdb.getPDBId();\r
- PDBEntry pdbentry = null;\r
- if (pdbe != null && pdbe.size() > 0)\r
- {\r
- for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)\r
- {\r
- pdbentry = (PDBEntry) pdbe.elementAt(pe);\r
- if (!pdbentry.getId().equals(pdbEntryString)\r
- && !pdbentry.getFile().equals(pdbFile))\r
- {\r
- pdbentry = null;\r
- }\r
- else\r
- {\r
- continue;\r
- }\r
- }\r
- }\r
- if (pdbentry == null)\r
- {\r
- pdbentry = new PDBEntry();\r
- pdbentry.setId(pdbEntryString);\r
- pdbentry.setFile(pdbFile);\r
- needtoadd = true; // add this new entry to sequence.\r
- }\r
- // resolve data source\r
- // TODO: this code should be a refactored to an io package\r
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");\r
- if (protocol == null)\r
- {\r
- return false;\r
- }\r
- if (needtoadd)\r
- {\r
- // make a note of the access mode and add\r
- if (pdbentry.getProperty() == null)\r
- {\r
- pdbentry.setProperty(new Hashtable());\r
- }\r
- pdbentry.getProperty().put("protocol", protocol);\r
- toaddpdb.addPDBId(pdbentry);\r
- }\r
- }\r
- return true;\r
- }\r
-\r
- private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)\r
- {\r
- if (seqs != null)\r
- {\r
- Vector sequences = new Vector();\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i] != null)\r
- {\r
- sequences.addElement(new Object[]\r
- { seqs[i], (chains != null) ? chains[i] : null });\r
- }\r
- }\r
- seqs = new SequenceI[sequences.size()];\r
- chains = new String[sequences.size()];\r
- for (int i = 0, isize = sequences.size(); i < isize; i++)\r
- {\r
- Object[] oj = (Object[]) sequences.elementAt(i);\r
-\r
- seqs[i] = (SequenceI) oj[0];\r
- chains[i] = (String) oj[1];\r
- }\r
- }\r
- return new Object[]\r
- { seqs, chains };\r
-\r
- }\r
-\r
- public void newStructureView(JalviewLite applet, PDBEntry pdb,\r
- SequenceI[] seqs, String[] chains, String protocol)\r
- {\r
- // Scrub any null sequences from the array\r
- Object[] sqch = cleanSeqChainArrays(seqs, chains);\r
- seqs = (SequenceI[]) sqch[0];\r
- chains = (String[]) sqch[1];\r
- if (seqs == null || seqs.length == 0)\r
- {\r
- System.err\r
- .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");\r
- }\r
- if (protocol == null || protocol.trim().length() == 0\r
- || protocol.equals("null"))\r
- {\r
- protocol = (String) pdb.getProperty().get("protocol");\r
- if (protocol == null)\r
- {\r
- System.err.println("Couldn't work out protocol to open structure: "\r
- + pdb.getId());\r
- return;\r
- }\r
- }\r
- if (applet.useXtrnalSviewer)\r
- {\r
- // register the association(s) and quit, don't create any windows.\r
- if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
- System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
- }\r
- return;\r
- }\r
- if (applet.isAlignPdbStructures() && applet.jmolAvailable)\r
- {\r
- // can only do alignments with Jmol\r
- // find the last jmol window assigned to this alignment\r
- jalview.appletgui.AppletJmol ajm = null, tajm;\r
- Vector jmols = applet\r
- .getAppletWindow(jalview.appletgui.AppletJmol.class);\r
- for (int i = 0, iSize = jmols.size(); i < iSize; i++)\r
- {\r
- tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);\r
- if (tajm.ap.alignFrame == this)\r
- {\r
- ajm = tajm;\r
- break;\r
- }\r
- }\r
- if (ajm != null)\r
- {\r
- System.err\r
- .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");\r
- // try and add the pdb structure\r
- // ajm.addS\r
- ajm = null;\r
- }\r
- }\r
- // otherwise, create a new window\r
- if (applet.jmolAvailable)\r
- {\r
- new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,\r
- protocol);\r
- applet.lastFrameX += 40;\r
- applet.lastFrameY += 40;\r
- }\r
- else\r
- {\r
- new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);\r
- }\r
-\r
- }\r
-\r
- public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,\r
- SequenceI[][] seqs, String[][] chains, String[] protocols)\r
- {\r
- // TODO Auto-generated method stub\r
- System.err.println("Aligned Structure View: Not yet implemented.");\r
- }\r
-\r
- /**\r
- * modify the current selection, providing the user has not made a selection already.\r
- * @param sel - sequences from this alignment\r
- * @param csel - columns to be selected on the alignment\r
- */\r
- public void select(SequenceGroup sel, ColumnSelection csel)\r
- {\r
- alignPanel.seqPanel.selection(sel, csel, null);\r
- }\r
-\r
- public void scrollTo(int row, int column)\r
- {\r
- alignPanel.seqPanel.scrollTo(row, column);\r
- }\r
- public void scrollToRow(int row)\r
- {\r
- alignPanel.seqPanel.scrollToRow(row);\r
- }\r
- public void scrollToColumn(int column)\r
- {\r
- alignPanel.seqPanel.scrollToColumn(column);\r
- }\r
- /**\r
- * @return the alignments unique ID.\r
- */\r
- public String getSequenceSetId() {\r
- return viewport.getSequenceSetId();\r
- }\r
-\r
-\r
- /**\r
- * Load the (T-Coffee) score file from the specified url\r
- *\r
- * @param source File/URL/T-COFFEE score file contents\r
- * @throws IOException\r
- * @return true if alignment was annotated with data from source\r
- */\r
- public boolean loadScoreFile( String source ) throws IOException {\r
-\r
- TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
- if( !file.isValid()) {\r
- // TODO: raise dialog for gui\r
- System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());\r
- System.err.println("Origin was:\n"+source);\r
- return false;\r
- }\r
-\r
- /*\r
- * check that the score matrix matches the alignment dimensions\r
- */\r
- AlignmentI aln;\r
- if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
- // TODO: raise a dialog box here rather than bomb out.\r
- System.err.println("The scores matrix does not match the alignment dimensions");\r
-\r
- }\r
-\r
- // TODO add parameter to indicate if matching should be done\r
- if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
- {\r
- alignPanel.fontChanged();\r
- tcoffeeColour.setEnabled(true);\r
- // switch to this color\r
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
- return true;\r
- } else {\r
- System.err.println("Problems resolving T-Coffee scores:");\r
- if (file.getWarningMessage()!=null) {\r
- System.err.println(file.getWarningMessage());\r
- }\r
- }\r
- return false;\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SequenceStructureBinding;
+import jalview.bin.JalviewLite;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.jmol.viewer.Viewer;
+
+public class AlignFrame extends EmbmenuFrame implements ActionListener,
+ ItemListener, KeyListener, AlignViewControllerGuiI
+{
+ public AlignViewControllerI avc;
+
+ public AlignmentPanel alignPanel;
+
+ public AlignViewport viewport;
+
+ // width and height may be overridden by applet parameters
+ int frameWidth = 700;
+
+ int frameHeight = 500;
+
+ String jalviewServletURL;
+
+ /*
+ * Flag for showing autocalculated consensus above or below other consensus
+ * rows
+ */
+ private boolean showAutoCalculatedAbove;
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ /**
+ * Constructor that creates the frame and adds it to the display.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded)
+ {
+ this(al, applet, title, embedded, true);
+ }
+
+ /**
+ * Constructor that optionally allows the frame to be displayed or only
+ * created.
+ *
+ * @param al
+ * @param applet
+ * @param title
+ * @param embedded
+ * @param addToDisplay
+ */
+ public AlignFrame(AlignmentI al, JalviewLite applet, String title,
+ boolean embedded, boolean addToDisplay)
+ {
+ this(al, null, null, applet, title, embedded, addToDisplay);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded)
+ {
+ this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ }
+
+ public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+ ColumnSelection columnSelection, JalviewLite applet,
+ String title, boolean embedded, boolean addToDisplay)
+ {
+ if (applet != null)
+ {
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ // need to get window geometry before we calculate alignment layout
+ if (applet != null)
+ {
+ String param;
+ try
+ {
+ param = applet.getParameter("windowWidth");
+ if (param != null)
+ {
+ int width = Integer.parseInt(param);
+ frameWidth = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ frameHeight = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
+ viewport = new AlignViewport(al, applet);
+
+ if (hiddenSeqs != null && hiddenSeqs.length > 0)
+ {
+ viewport.hideSequence(hiddenSeqs);
+ }
+ if (columnSelection != null)
+ {
+ viewport.setColumnSelection(columnSelection);
+ }
+
+ alignPanel = new AlignmentPanel(this, viewport);
+ avc = new jalview.controller.AlignViewController(this, viewport,
+ alignPanel);
+ viewport.updateConservation(alignPanel);
+ viewport.updateConsensus(alignPanel);
+
+ displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
+ followMouseOverFlag.setState(viewport.isFollowHighlight());
+ showGroupConsensus.setState(viewport.isShowGroupConsensus());
+ showGroupConservation.setState(viewport.isShowGroupConservation());
+ showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+ showSequenceLogo.setState(viewport.isShowSequenceLogo());
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
+ applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+ annotationPanelMenuItem.setState(viewport.isShowAnnotation());
+ showAlignmentAnnotations.setState(viewport.isShowAnnotation());
+ showSequenceAnnotations.setState(viewport.isShowAnnotation());
+
+ seqLimits.setState(viewport.getShowJVSuffix());
+
+ if (applet != null)
+ {
+ String param = applet.getParameter("sortBy");
+ if (param != null)
+ {
+ if (param.equalsIgnoreCase("Id"))
+ {
+ sortIDMenuItem_actionPerformed();
+ }
+ else if (param.equalsIgnoreCase("Pairwise Identity"))
+ {
+ sortPairwiseMenuItem_actionPerformed();
+ }
+ else if (param.equalsIgnoreCase("Length"))
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
+ }
+
+ param = applet.getParameter("wrap");
+ if (param != null)
+ {
+ if (param.equalsIgnoreCase("true"))
+ {
+ wrapMenuItem.setState(true);
+ wrapMenuItem_actionPerformed();
+ }
+ }
+ param = applet.getParameter("centrecolumnlabels");
+ if (param != null)
+ {
+ centreColumnLabelFlag.setState(true);
+ centreColumnLabelFlag_stateChanged();
+ }
+
+ }
+ if (viewport.getAlignment().isNucleotide())
+ {
+ viewport.updateStrucConsensus(alignPanel);
+ if (viewport.getAlignment().hasRNAStructure())
+ {
+ RNAHelixColour.setEnabled(true);
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ }
+ }
+ else
+ {
+ RNAHelixColour.setEnabled(false);
+ purinePyrimidineColour.setEnabled(false);
+ }
+ // Some JVMS send keyevents to Top frame or lowest panel,
+ // Havent worked out why yet. So add to both this frame and seqCanvas for
+ // now
+ this.addKeyListener(this);
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);
+ alignPanel.idPanel.idCanvas.addKeyListener(this);
+ alignPanel.scalePanel.addKeyListener(this);
+ alignPanel.annotationPanel.addKeyListener(this);
+ alignPanel.annotationPanelHolder.addKeyListener(this);
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+ alignPanel.alabels.addKeyListener(this);
+
+ if (addToDisplay)
+ {
+ addToDisplay(embedded);
+ }
+ }
+
+ /**
+ * @param embedded
+ */
+ public void addToDisplay(boolean embedded)
+ {
+ createAlignFrameWindow(embedded);
+ validate();
+ alignPanel.adjustAnnotationHeight();
+ alignPanel.paintAlignment(true);
+ }
+
+ public AlignViewport getAlignViewport()
+ {
+ return viewport;
+ }
+
+ public SeqCanvas getSeqcanvas()
+ {
+ return alignPanel.seqPanel.seqCanvas;
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
+ */
+
+ public boolean parseFeaturesFile(String file, String type)
+ {
+ return parseFeaturesFile(file, type, true);
+ }
+
+ /**
+ * Load a features file onto the alignment
+ *
+ * @param file
+ * file URL, content, or other resolvable path
+ * @param type
+ * is protocol for accessing data referred to by file
+ * @param autoenabledisplay
+ * when true, display features flag will be automatically enabled if
+ * features are loaded
+ * @return true if data parsed as a features file
+ */
+ public boolean parseFeaturesFile(String file, String type,
+ boolean autoenabledisplay)
+ {
+ // TODO: test if importing a features file onto an alignment which already
+ // has features with links overwrites the original links.
+
+ Hashtable featureLinks = new Hashtable();
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
+ .getAlignment(), alignPanel.seqPanel.seqCanvas
+ .getFeatureRenderer().getFeatureColours(), featureLinks,
+ true, viewport.applet.getDefaultParameter("relaxedidmatch",
+ false));
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ if (featureLinks.size() > 0)
+ {
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
+ }
+ if (autoenabledisplay)
+ {
+ viewport.setShowSequenceFeatures(true);
+ sequenceFeatures.setState(true);
+ }
+ if (alignPanel.seqPanel.seqCanvas.fr != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+ }
+ if (viewport.featureSettings != null)
+ {
+ viewport.featureSettings.refreshTable();
+ }
+ alignPanel.paintAlignment(true);
+ statusBar.setText(MessageManager
+ .getString("label.successfully_added_features_alignment"));
+ }
+ return featuresFile;
+ }
+
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (viewport.cursorMode
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))
+ && Character.isDigit(evt.getKeyChar()))
+ {
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
+
+ switch (evt.getKeyCode())
+ {
+ case 27: // escape key
+ deselectAllSequenceMenuItem_actionPerformed();
+
+ alignPanel.alabels.cancelDrag();
+ break;
+ case KeyEvent.VK_X:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ cut_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_C:
+ if (viewport.cursorMode && !evt.isControlDown())
+ {
+ alignPanel.seqPanel.setCursorColumn();
+ }
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ copy_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_V:
+ if (evt.isControlDown())
+ {
+ paste(evt.isShiftDown());
+ }
+ break;
+ case KeyEvent.VK_A:
+ if (evt.isControlDown() || evt.isMetaDown())
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ break;
+ case KeyEvent.VK_DOWN:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, 1);
+ }
+ else
+ {
+ moveSelectedSequences(false);
+ }
+ break;
+
+ case KeyEvent.VK_UP:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.moveCursor(0, -1);
+ }
+ else
+ {
+ moveSelectedSequences(true);
+ }
+ break;
+
+ case KeyEvent.VK_LEFT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.seqPanel.moveCursor(-1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_RIGHT:
+ if (evt.isAltDown() || !viewport.cursorMode)
+ {
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
+ else
+ {
+ alignPanel.seqPanel.moveCursor(1, 0);
+ }
+ break;
+
+ case KeyEvent.VK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ break;
+
+ case KeyEvent.VK_DELETE:
+ case KeyEvent.VK_BACK_SPACE:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+ || evt.isShiftDown() || evt.isAltDown());
+ }
+ else
+ {
+ cut_actionPerformed();
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ break;
+
+ case KeyEvent.VK_S:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRow();
+ }
+ break;
+ case KeyEvent.VK_P:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorPosition();
+ }
+ break;
+
+ case KeyEvent.VK_ENTER:
+ case KeyEvent.VK_COMMA:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setCursorRowAndColumn();
+ }
+ break;
+
+ case KeyEvent.VK_Q:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+ }
+ break;
+ case KeyEvent.VK_M:
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+ }
+ break;
+
+ case KeyEvent.VK_F2:
+ viewport.cursorMode = !viewport.cursorMode;
+ statusBar.setText(MessageManager.formatMessage(
+ "label.keyboard_editing_mode",
+ new String[] { (viewport.cursorMode ? "on" : "off") }));
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+ }
+ break;
+
+ case KeyEvent.VK_F:
+ if (evt.isControlDown())
+ {
+ findMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_H:
+ {
+ boolean toggleSeqs = !evt.isControlDown();
+ boolean toggleCols = !evt.isShiftDown();
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
+ }
+
+ case KeyEvent.VK_PAGE_UP:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(true);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ - viewport.endSeq + viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_PAGE_DOWN:
+ if (viewport.getWrapAlignment())
+ {
+ alignPanel.scrollUp(false);
+ }
+ else
+ {
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
+ + viewport.endSeq - viewport.startSeq);
+ }
+ break;
+
+ case KeyEvent.VK_Z:
+ if (evt.isControlDown())
+ {
+ undoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_Y:
+ if (evt.isControlDown())
+ {
+ redoMenuItem_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_L:
+ if (evt.isControlDown())
+ {
+ trimAlignment(true);
+ }
+ break;
+
+ case KeyEvent.VK_R:
+ if (evt.isControlDown())
+ {
+ trimAlignment(false);
+ }
+ break;
+
+ case KeyEvent.VK_E:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.removeAllGapsMenuItem_actionPerformed();
+ }
+ else
+ {
+ removeGappedColumnMenuItem_actionPerformed();
+ }
+ }
+ break;
+ case KeyEvent.VK_I:
+ if (evt.isControlDown())
+ {
+ if (evt.isAltDown())
+ {
+ invertColSel_actionPerformed();
+ }
+ else
+ {
+ invertSequenceMenuItem_actionPerformed();
+ }
+ }
+ break;
+
+ case KeyEvent.VK_G:
+ if (evt.isControlDown())
+ {
+ if (evt.isShiftDown())
+ {
+ this.unGroup_actionPerformed();
+ }
+ else
+ {
+ this.createGroup_actionPerformed();
+ }
+ }
+ break;
+
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
+
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.getColumnSelection() != null
+ && viewport.getColumnSelection().getSelected() != null && viewport
+ .getColumnSelection().getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed();
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection and indicate it should be hidden.
+ invertColSel_actionPerformed();
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
+ {
+ hide = true;
+ viewport.hideAllSelectedSeqs();
+ }
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+ .size() > 0))
+ {
+ viewport.showAllHiddenSeqs();
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.getColumnSelection().getSelected().size() > 0)
+ {
+ viewport.hideSelectedColumns();
+ if (!toggleSeqs)
+ {
+ viewport.setSelectionGroup(sg);
+ }
+ }
+ else if (!hide)
+ {
+ viewport.showAllHiddenColumns();
+ }
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ @Override
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ final Object source = evt.getSource();
+ if (source == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else if (source == colourTextMenuItem)
+ {
+ colourTextMenuItem_actionPerformed();
+ }
+ else if (source == wrapMenuItem)
+ {
+ wrapMenuItem_actionPerformed();
+ }
+ else if (source == scaleAbove)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
+ }
+ else if (source == scaleLeft)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.getState());
+ }
+ else if (source == scaleRight)
+ {
+ viewport.setScaleRightWrapped(scaleRight.getState());
+ }
+ else if (source == seqLimits)
+ {
+ seqLimits_itemStateChanged();
+ }
+ else if (source == viewBoxesMenuItem)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());
+ }
+ else if (source == viewTextMenuItem)
+ {
+ viewport.setShowText(viewTextMenuItem.getState());
+ }
+ else if (source == renderGapsMenuItem)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.getState());
+ }
+ else if (source == annotationPanelMenuItem)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ }
+ else if (source == sequenceFeatures)
+ {
+ viewport.setShowSequenceFeatures(sequenceFeatures.getState());
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ else if (source == showAlignmentAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == showSequenceAnnotations)
+ {
+ setAnnotationsVisibility();
+ }
+ else if (source == sortAnnBySequence)
+ {
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == sortAnnByLabel)
+ {
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setState(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoFirst)
+ {
+ showAutoLast.setState(!showAutoFirst.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == showAutoLast)
+ {
+ showAutoFirst.setState(!showAutoLast.getState());
+ setShowAutoCalculatedAbove(showAutoFirst.getState());
+ setViewportAnnotationOrder();
+ }
+ else if (source == conservationMenuItem)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ else if (source == abovePIDThreshold)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ else if (source == applyToAllGroups)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
+ }
+ else if (source == autoCalculate)
+ {
+ viewport.autoCalculateConsensus = autoCalculate.getState();
+ }
+ else if (source == sortByTree)
+ {
+ viewport.sortByTree = sortByTree.getState();
+ }
+ else if (source == this.centreColumnLabelFlag)
+ {
+ centreColumnLabelFlag_stateChanged();
+ }
+ else if (source == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Set the visibility state of sequence-related and/or alignment-related
+ * annotations depending on checkbox selections. Repaint after calling.
+ *
+ * @param visible
+ */
+ private void setAnnotationsVisibility()
+ {
+ boolean showForAlignment = showAlignmentAnnotations.getState();
+ boolean showForSequences = showSequenceAnnotations.getState();
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ boolean visible = (aa.sequenceRef == null ? showForAlignment
+ : showForSequences);
+ aa.visible = visible;
+ }
+ alignPanel.validateAnnotationDimensions(true);
+ validate();
+ repaint();
+ }
+
+ private void setAnnotationSortOrder(SequenceAnnotationOrder order)
+ {
+ this.annotationSortOrder = order;
+ }
+
+ /**
+ * Set flags on the viewport that control annotation ordering
+ */
+ private void setViewportAnnotationOrder()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
+ }
+
+ private void setShowAutoCalculatedAbove(boolean showAbove)
+ {
+ this.showAutoCalculatedAbove = showAbove;
+ }
+
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.setFollowHighlight(followMouseOverFlag.getState());
+ // TODO: could kick the scrollTo mechanism to reset view for current
+ // searchresults.
+ }
+
+ private void centreColumnLabelFlag_stateChanged()
+ {
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();
+ this.alignPanel.annotationPanel.repaint();
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ viewport.applet.currentAlignFrame = this;
+
+ Object source = evt.getSource();
+
+ if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == loadTree)
+ {
+ loadTree_actionPerformed();
+ }
+ else if (source == loadApplication)
+ {
+ launchFullApplication();
+ }
+ else if (source == loadAnnotations)
+ {
+ loadAnnotations();
+ }
+ else if (source == outputAnnotations)
+ {
+ outputAnnotations(true);
+ }
+ else if (source == outputFeatures)
+ {
+ outputFeatures(true, "Jalview");
+ }
+ else if (source == closeMenuItem)
+ {
+ closeMenuItem_actionPerformed();
+ }
+ else if (source == copy)
+ {
+ copy_actionPerformed();
+ }
+ else if (source == undoMenuItem)
+ {
+ undoMenuItem_actionPerformed();
+ }
+ else if (source == redoMenuItem)
+ {
+ redoMenuItem_actionPerformed();
+ }
+ else if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == closeMenuItem)
+ {
+ closeMenuItem_actionPerformed();
+ }
+ else if (source == undoMenuItem)
+ {
+ undoMenuItem_actionPerformed();
+ }
+ else if (source == redoMenuItem)
+ {
+ redoMenuItem_actionPerformed();
+ }
+ else if (source == copy)
+ {
+ copy_actionPerformed();
+ }
+ else if (source == pasteNew)
+ {
+ pasteNew_actionPerformed();
+ }
+ else if (source == pasteThis)
+ {
+ pasteThis_actionPerformed();
+ }
+ else if (source == cut)
+ {
+ cut_actionPerformed();
+ }
+ else if (source == delete)
+ {
+ delete_actionPerformed();
+ }
+ else if (source == grpsFromSelection)
+ {
+ makeGrpsFromSelection_actionPerformed();
+ }
+ else if (source == deleteGroups)
+ {
+ deleteGroups_actionPerformed();
+ }
+ else if (source == selectAllSequenceMenuItem)
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == deselectAllSequenceMenuItem)
+ {
+ deselectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertSequenceMenuItem)
+ {
+ invertSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertColSel)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == remove2LeftMenuItem)
+ {
+ trimAlignment(true);
+ }
+ else if (source == remove2RightMenuItem)
+ {
+ trimAlignment(false);
+ }
+ else if (source == removeGappedColumnMenuItem)
+ {
+ removeGappedColumnMenuItem_actionPerformed();
+ }
+ else if (source == removeAllGapsMenuItem)
+ {
+ removeAllGapsMenuItem_actionPerformed();
+ }
+ else if (source == findMenuItem)
+ {
+ findMenuItem_actionPerformed();
+ }
+ else if (source == font)
+ {
+ new FontChooser(alignPanel);
+ }
+ else if (source == newView)
+ {
+ newView(null);
+ }
+ else if (source == showColumns)
+ {
+ viewport.showAllHiddenColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showSeqs)
+ {
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideColumns)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
+ {
+ viewport.hideAllSelectedSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllButSelection)
+ {
+ toggleHiddenRegions(false, false);
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideAllSelection)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showAllHidden)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showGroupConsensus)
+ {
+ showGroupConsensus_actionPerformed();
+ }
+ else if (source == showGroupConservation)
+ {
+ showGroupConservation_actionPerformed();
+ }
+ else if (source == showSequenceLogo)
+ {
+ showSequenceLogo_actionPerformed();
+ }
+ else if (source == normSequenceLogo)
+ {
+ normSequenceLogo_actionPerformed();
+ }
+ else if (source == showConsensusHistogram)
+ {
+ showConsensusHistogram_actionPerformed();
+ }
+ else if (source == applyAutoAnnotationSettings)
+ {
+ applyAutoAnnotationSettings_actionPerformed();
+ }
+ else if (source == featureSettings)
+ {
+ new FeatureSettings(alignPanel);
+ }
+ else if (source == alProperties)
+ {
+ StringBuffer contents = new jalview.io.AlignmentProperties(
+ viewport.getAlignment()).formatAsString();
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ cap.setText(contents.toString());
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_properties", new String[] { getTitle() }),
+ 400, 250);
+ }
+ else if (source == overviewMenuItem)
+ {
+ overviewMenuItem_actionPerformed();
+ }
+ else if (source == noColourmenuItem)
+ {
+ changeColour(null);
+ }
+ else if (source == clustalColour)
+ {
+ abovePIDThreshold.setState(false);
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
+ }
+ 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 == purinePyrimidineColour)
+ {
+ changeColour(new PurinePyrimidineColourScheme());
+ }
+ // else if (source == RNAInteractionColour)
+ // {
+ // changeColour(new RNAInteractionColourScheme());
+ // }
+ else if (source == RNAHelixColour)
+ {
+ new RNAHelicesColourChooser(viewport, alignPanel);
+ }
+ 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 == tcoffeeColour)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ }
+ else if (source == annotationColour)
+ {
+ new AnnotationColourChooser(viewport, alignPanel);
+ }
+ else if (source == annotationColumnSelection)
+ {
+ new AnnotationColumnChooser(viewport, alignPanel);
+ }
+ else if (source == sortPairwiseMenuItem)
+ {
+ sortPairwiseMenuItem_actionPerformed();
+ }
+ else if (source == sortIDMenuItem)
+ {
+ sortIDMenuItem_actionPerformed();
+ }
+ else if (source == sortLengthMenuItem)
+ {
+ sortLengthMenuItem_actionPerformed();
+ }
+ else if (source == sortGroupMenuItem)
+ {
+ sortGroupMenuItem_actionPerformed();
+ }
+ else if (source == removeRedundancyMenuItem)
+ {
+ removeRedundancyMenuItem_actionPerformed();
+ }
+ else if (source == pairwiseAlignmentMenuItem)
+ {
+ pairwiseAlignmentMenuItem_actionPerformed();
+ }
+ else if (source == PCAMenuItem)
+ {
+ PCAMenuItem_actionPerformed();
+ }
+ else if (source == averageDistanceTreeMenuItem)
+ {
+ averageDistanceTreeMenuItem_actionPerformed();
+ }
+ else if (source == neighbourTreeMenuItem)
+ {
+ neighbourTreeMenuItem_actionPerformed();
+ }
+ else if (source == njTreeBlosumMenuItem)
+ {
+ njTreeBlosumMenuItem_actionPerformed();
+ }
+ else if (source == avDistanceTreeBlosumMenuItem)
+ {
+ avTreeBlosumMenuItem_actionPerformed();
+ }
+ else if (source == documentation)
+ {
+ documentation_actionPerformed();
+ }
+ else if (source == about)
+ {
+ about_actionPerformed();
+ }
+
+ }
+
+ public void inputText_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.input_cut_paste"), 500, 500);
+ }
+
+ protected void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.alignment_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
+
+ FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+ cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
+ e.getActionCommand(), viewport.getAlignment(),
+ viewport.getShowJVSuffix()));
+ }
+
+ public void loadAnnotations()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ cap.setText(MessageManager
+ .getString("label.paste_features_annotations_Tcoffee_here"));
+ cap.setAnnotationImport();
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.paste_annotations"), 400, 300);
+
+ }
+
+ public String outputAnnotations(boolean displayTextbox)
+ {
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(viewport);
+
+ if (displayTextbox)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.annotations"), 600, 500);
+ cap.setText(annotation);
+ }
+
+ return annotation;
+ }
+
+ private Map<String, Object> getDisplayedFeatureCols()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
+
+ }
+ return null;
+ }
+
+ public String outputFeatures(boolean displayTextbox, String format)
+ {
+ String features;
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = new FeaturesFile().printJalviewFormat(viewport
+ .getAlignment().getSequencesArray(),
+ getDisplayedFeatureCols());
+ }
+ else
+ {
+ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols());
+ }
+
+ if (displayTextbox)
+ {
+ boolean frimport = false;
+ if (features == null || features.equals("No Features Visible"))
+ {
+ features = "# No features visible - paste some and import them here.";
+ frimport = true;
+ }
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+ if (frimport)
+ {
+ cap.setAnnotationImport();
+ }
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.features"), 600, 500);
+ cap.setText(features);
+ }
+ else
+ {
+ if (features == null)
+ {
+ features = "";
+ }
+ }
+
+ return features;
+ }
+
+ void launchFullApplication()
+ {
+ StringBuffer url = new StringBuffer(jalviewServletURL);
+
+ // allow servlet parameters to be passed in applet parameter
+ String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
+ : "?";
+ url.append(firstSep);
+
+ url.append("open="
+ + appendProtocol(viewport.applet.getParameter("file")));
+
+ if (viewport.applet.getParameter("features") != null)
+ {
+ url.append("&features=");
+ url.append(appendProtocol(viewport.applet.getParameter("features")));
+ }
+
+ if (viewport.applet.getParameter("annotations") != null)
+ {
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));
+ }
+
+ if (viewport.applet.getParameter("jnetfile") != null)
+ {
+ url.append("&annotations=");
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+ }
+
+ if (viewport.applet.getParameter("defaultColour") != null)
+ {
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("defaultColour")));
+ }
+
+ if (viewport.applet.getParameter("userDefinedColour") != null)
+ {
+ url.append("&colour="
+ + removeWhiteSpace(viewport.applet
+ .getParameter("userDefinedColour")));
+ }
+ if (viewport.applet.getParameter("tree") != null)
+ {
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("tree")));
+ }
+ if (viewport.applet.getParameter("treeFile") != null)
+ {
+ url.append("&tree="
+ + appendProtocol(viewport.applet.getParameter("treeFile")));
+ }
+
+ showURL(url.toString(), "FULL_APP");
+ }
+
+ String removeWhiteSpace(String colour)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < colour.length(); i++)
+ {
+ if (Character.isWhitespace(colour.charAt(i)))
+ {
+ sb.append("%20");
+ }
+ else
+ {
+ sb.append(colour.charAt(i));
+ }
+ }
+
+ return sb.toString();
+ }
+
+ String appendProtocol(String url)
+ {
+ try
+ {
+ new URL(url);
+ url = URLEncoder.encode(url);
+ }
+ /*
+ * When we finally deprecate 1.1 compatibility, we can start to use
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
+ * ex.printStackTrace(); }
+ */
+ catch (java.net.MalformedURLException ex)
+ {
+ url = viewport.applet.getCodeBase() + url;
+ }
+ return url;
+ }
+
+ public void closeMenuItem_actionPerformed()
+ {
+ PaintRefresher.RemoveComponent(alignPanel);
+ if (alignPanel.seqPanel != null
+ && alignPanel.seqPanel.seqCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+ }
+ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
+ {
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+ }
+
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)
+ {
+ System.exit(0);
+ }
+ else
+ {
+ }
+ viewport = null;
+ alignPanel = null;
+ this.dispose();
+ }
+
+ /**
+ * TODO: JAL-1104
+ */
+ void updateEditMenuBar()
+ {
+
+ if (viewport.getHistoryList().size() > 0)
+ {
+ undoMenuItem.setEnabled(true);
+ CommandI command = viewport.getHistoryList().peek();
+ undoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.undo_command",
+ new Object[] { command.getDescription() }));
+ }
+ else
+ {
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
+ }
+
+ if (viewport.getRedoList().size() > 0)
+ {
+ redoMenuItem.setEnabled(true);
+
+ CommandI command = viewport.getRedoList().peek();
+ redoMenuItem.setLabel(MessageManager.formatMessage(
+ "label.redo_command",
+ new Object[] { command.getDescription() }));
+ }
+ else
+ {
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
+ }
+ }
+
+ /**
+ * TODO: JAL-1104
+ */
+ @Override
+ public void addHistoryItem(CommandI command)
+ {
+ if (command.getSize() > 0)
+ {
+ viewport.addToHistoryList(command);
+ viewport.clearRedoList();
+ updateEditMenuBar();
+ viewport.updateHiddenColumns();
+ }
+ }
+
+ /**
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void undoMenuItem_actionPerformed()
+ {
+ if (viewport.getHistoryList().isEmpty())
+ {
+ return;
+ }
+
+ CommandI command = viewport.getHistoryList().pop();
+ viewport.addToRedoList(command);
+ command.undoCommand(null);
+
+ AlignmentViewport originalSource = getOriginatingSource(command);
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst undoing");
+ }
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
+ updateEditMenuBar();
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
+ }
+
+ /**
+ * TODO: JAL-1104 DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void redoMenuItem_actionPerformed()
+ {
+ if (viewport.getRedoList().isEmpty())
+ {
+ return;
+ }
+
+ CommandI command = viewport.getRedoList().pop();
+ viewport.addToHistoryList(command);
+ command.doCommand(null);
+
+ AlignmentViewport originalSource = getOriginatingSource(command);
+ // JBPNote Test
+ if (originalSource != viewport)
+ {
+ System.err
+ .println("Warning: Viewport object mismatch whilst re-doing");
+ }
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
+ // viewport.getColumnSelection().getHiddenColumns()
+ // != null;
+
+ updateEditMenuBar();
+ originalSource.firePropertyChange("alignment", null, originalSource
+ .getAlignment().getSequences());
+ }
+
+ AlignmentViewport getOriginatingSource(CommandI command)
+ {
+ AlignmentViewport 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.getAlignment())
+ {
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+ break;
+ }
+ }
+ }
+ }
+
+ if (originalSource == null)
+ {
+ // The original view is closed, we must validate
+ // the current view against the closed view first
+ if (al != null)
+ {
+ PaintRefresher.validateSequences(al, viewport.getAlignment());
+ }
+
+ originalSource = viewport;
+ }
+
+ return originalSource;
+ }
+
+ /**
+ * Move the currently selected sequences up or down one position in the
+ * alignment
+ *
+ * @param up
+ */
+ public void moveSelectedSequences(boolean up)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,
+ up ? null : viewport.getHiddenRepSequences(), up);
+ alignPanel.paintAlignment(true);
+
+ /*
+ * Also move cDNA/protein complement sequences
+ */
+ AlignViewportI complement = viewport.getCodingComplement();
+ if (complement != null)
+ {
+ SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
+ viewport, complement);
+ complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
+ up ? null : complement.getHiddenRepSequences(), up);
+ // TODO need to trigger a repaint of the complementary panel - how?
+ // would prefer to handle in SplitFrame but it is not overriding key
+ // listener chiz
+ }
+ }
+
+ synchronized void slideSequences(boolean right, int size)
+ {
+ List<SequenceI> sg = new Vector<SequenceI>();
+ if (viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment().getSequenceAt(
+ alignPanel.seqPanel.seqCanvas.cursorY));
+ }
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() != viewport
+ .getAlignment().getHeight())
+ {
+ sg = viewport.getSelectionGroup().getSequences(
+ viewport.getHiddenRepSequences());
+ }
+
+ if (sg.size() < 1)
+ {
+ return;
+ }
+
+ Vector<SequenceI> invertGroup = new Vector();
+
+ for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+ {
+ if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
+ invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+ }
+ }
+
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
+
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
+ .size()]);
+ for (int i = 0; i < invertGroup.size(); i++)
+ {
+ seqs2[i] = 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;
+ Deque<CommandI> historyList = viewport.getHistoryList();
+ if (historyList != null && historyList.size() > 0
+ && historyList.peek() instanceof SlideSequencesCommand)
+ {
+ appendHistoryItem = ssc
+ .appendSlideCommand((SlideSequencesCommand) historyList
+ .peek());
+ }
+
+ if (!appendHistoryItem)
+ {
+ addHistoryItem(ssc);
+ }
+
+ repaint();
+ }
+
+ static StringBuffer copiedSequences;
+
+ static Vector copiedHiddenColumns;
+
+ protected void copy_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ copiedSequences = new StringBuffer();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ SequenceI seq = sg.getSequenceAt(i);
+ int index = viewport.getAlignment().findIndex(seq);
+ orderedSeqs.put(index, seq);
+ }
+
+ int index = 0, startRes, endRes;
+ char ch;
+
+ if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
+ {
+ copiedHiddenColumns = new Vector();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ {
+ copiedHiddenColumns.addElement(new int[] {
+ region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
+ }
+ else
+ {
+ copiedHiddenColumns = null;
+ }
+
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ SequenceI seq = null;
+
+ while (seq == null)
+ {
+ if (orderedSeqs.containsKey(index))
+ {
+ seq = orderedSeqs.get(index);
+ index++;
+ break;
+ }
+ else
+ {
+ index++;
+ }
+ }
+
+ // FIND START RES
+ // Returns residue following index if gap
+ startRes = seq.findPosition(sg.getStartRes());
+
+ // FIND END RES
+ // Need to find the residue preceeding index if gap
+ endRes = 0;
+
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+ {
+ ch = seq.getCharAt(j);
+ if (!jalview.util.Comparison.isGap((ch)))
+ {
+ endRes++;
+ }
+ }
+
+ if (endRes > 0)
+ {
+ endRes += seq.getStart() - 1;
+ }
+
+ copiedSequences.append(seq.getName()
+ + "\t"
+ + startRes
+ + "\t"
+ + endRes
+ + "\t"
+ + seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1) + "\n");
+ }
+
+ }
+
+ protected void pasteNew_actionPerformed()
+ {
+ paste(true);
+ }
+
+ protected void pasteThis_actionPerformed()
+ {
+ paste(false);
+ }
+
+ void paste(boolean newAlignment)
+ {
+ try
+ {
+
+ if (copiedSequences == null)
+ {
+ return;
+ }
+
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ Vector seqs = new Vector();
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+ int start = Integer.parseInt(st.nextToken());
+ int end = Integer.parseInt(st.nextToken());
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));
+ }
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ if (newAlignment)
+ {
+ String newtitle = MessageManager
+ .getString("label.copied_sequences");
+ if (getTitle().startsWith(
+ MessageManager.getString("label.copied_sequences")))
+ {
+ newtitle = getTitle();
+ }
+ else
+ {
+ newtitle = newtitle.concat(MessageManager.formatMessage(
+ "label.from_msname", new String[] { getTitle() }));
+ }
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),
+ viewport.applet, newtitle, false);
+ if (copiedHiddenColumns != null)
+ {
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)
+ {
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+ af.viewport.hideColumns(region[0], region[1]);
+ }
+ }
+
+ jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+ frameHeight);
+ }
+ else
+ {
+ addSequences(newSeqs);
+ }
+
+ } catch (Exception ex)
+ {
+ } // could be anything being pasted in here
+
+ }
+
+ void addSequences(SequenceI[] seqs)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ viewport.getAlignment().addSequence(seqs[i]);
+ }
+
+ // !newAlignment
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
+ seqs, 0, viewport.getAlignment().getWidth(),
+ viewport.getAlignment()));
+
+ viewport.setEndSeq(viewport.getAlignment().getHeight());
+ viewport.getAlignment().getWidth();
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ protected void cut_actionPerformed()
+ {
+ copy_actionPerformed();
+ delete_actionPerformed();
+ }
+
+ protected void delete_actionPerformed()
+ {
+
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ Vector seqs = new Vector();
+ SequenceI seq;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ seq = sg.getSequenceAt(i);
+ seqs.addElement(seq);
+ }
+
+ // If the cut affects all sequences, remove highlighted columns
+ if (sg.getSize() == viewport.getAlignment().getHeight())
+ {
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),
+ sg.getEndRes() + 1);
+ }
+
+ SequenceI[] cut = new SequenceI[seqs.size()];
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ cut[i] = (SequenceI) seqs.elementAt(i);
+ }
+
+ /*
+ * //ADD HISTORY ITEM
+ */
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ this.setVisible(false);
+ }
+ viewport.sendSelection();
+ }
+
+ /**
+ * group consensus toggled
+ *
+ */
+ protected void showGroupConsensus_actionPerformed()
+ {
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
+ }
+
+ /**
+ * group conservation toggled.
+ */
+ protected void showGroupConservation_actionPerformed()
+ {
+ viewport.setShowGroupConservation(showGroupConservation.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed()
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed()
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void normSequenceLogo_actionPerformed()
+ {
+ showSequenceLogo.setState(true);
+ viewport.setShowSequenceLogo(true);
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed()
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed()
+ {
+ if (avc.makeGroupsFromSelection())
+ {
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
+ }
+
+ protected void createGroup_actionPerformed()
+ {
+ avc.createGroup();
+ }
+
+ protected void unGroup_actionPerformed()
+ {
+ if (avc.unGroup())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ protected void deleteGroups_actionPerformed()
+ {
+ if (avc.deleteGroups())
+ {
+ alignPanel.alignmentChanged();
+ }
+ }
+
+ public void selectAllSequenceMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = new SequenceGroup();
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
+ }
+ sg.setEndRes(viewport.getAlignment().getWidth() - 1);
+ viewport.setSelectionGroup(sg);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ public void deselectAllSequenceMenuItem_actionPerformed()
+ {
+ if (viewport.cursorMode)
+ {
+ alignPanel.seqPanel.keyboardNo1 = null;
+ alignPanel.seqPanel.keyboardNo2 = null;
+ }
+ viewport.setSelectionGroup(null);
+ viewport.getColumnSelection().clear();
+ viewport.setSelectionGroup(null);
+ alignPanel.idPanel.idCanvas.searchResults = null;
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ public void invertSequenceMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
+ }
+
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ public void invertColSel_actionPerformed()
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
+ }
+
+ void trimAlignment(boolean trimLeft)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ int column;
+
+ if (colSel.size() > 0)
+ {
+ if (trimLeft)
+ {
+ column = colSel.getMin();
+ }
+ else
+ {
+ column = colSel.getMax();
+ }
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ TrimRegionCommand trimRegion;
+ if (trimLeft)
+ {
+ trimRegion = new TrimRegionCommand("Remove Left",
+ TrimRegionCommand.TRIM_LEFT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
+ viewport.setStartRes(0);
+ }
+ else
+ {
+ trimRegion = new TrimRegionCommand("Remove Right",
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,
+ viewport.getAlignment(), viewport.getColumnSelection(),
+ viewport.getSelectionGroup());
+ }
+
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_columns",
+ new String[] { Integer.valueOf(trimRegion.getSize())
+ .toString() }));
+ addHistoryItem(trimRegion);
+
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())
+ {
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))
+ {
+ viewport.getAlignment().deleteGroup(sg);
+ }
+ }
+
+ viewport.firePropertyChange("alignment", null, viewport
+ .getAlignment().getSequences());
+ }
+ }
+
+ public void removeGappedColumnMenuItem_actionPerformed()
+ {
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
+ "Remove Gapped Columns", seqs, start, end,
+ viewport.getAlignment());
+
+ addHistoryItem(removeGapCols);
+
+ statusBar.setText(MessageManager.formatMessage(
+ "label.removed_empty_columns",
+ new String[] { Integer.valueOf(removeGapCols.getSize())
+ .toString() }));
+
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+ // ShiftList shifts;
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());
+ // edit.alColumnChanges=shifts.getInverse();
+ // if (viewport.hasHiddenColumns)
+ // viewport.getColumnSelection().compensateForEdits(shifts);
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ public void removeAllGapsMenuItem_actionPerformed()
+ {
+ int start = 0, end = viewport.getAlignment().getWidth() - 1;
+
+ SequenceI[] seqs;
+ if (viewport.getSelectionGroup() != null)
+ {
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(
+ viewport.getHiddenRepSequences());
+ start = viewport.getSelectionGroup().getStartRes();
+ end = viewport.getSelectionGroup().getEndRes();
+ }
+ else
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+
+ // This is to maintain viewport position on first residue
+ // of first sequence
+ SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+ int startRes = seq.findPosition(viewport.startRes);
+
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
+ viewport.getAlignment()));
+
+ viewport.setStartRes(seq.findIndex(startRes) - 1);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()
+ .getSequences());
+
+ }
+
+ public void findMenuItem_actionPerformed()
+ {
+ new Finder(alignPanel);
+ }
+
+ /**
+ * create a new view derived from the current view
+ *
+ * @param viewtitle
+ * @return frame for the new view
+ */
+ public AlignFrame newView(String viewtitle)
+ {
+ AlignmentI newal;
+ if (viewport.hasHiddenRows())
+ {
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()
+ .getFullAlignment().getSequencesArray());
+ }
+ else
+ {
+ newal = new Alignment(viewport.getAlignment().getSequencesArray());
+ }
+
+ if (viewport.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
+ {
+ newal.addAnnotation(viewport.getAlignment()
+ .getAlignmentAnnotation()[i]);
+ }
+ }
+ }
+
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
+
+ newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
+ newaf.alignPanel.av.getSequenceSetId());
+
+ Vector comps = (Vector) PaintRefresher.components.get(viewport
+ .getSequenceSetId());
+ int viewSize = -1;
+ for (int i = 0; i < comps.size(); i++)
+ {
+ if (comps.elementAt(i) instanceof AlignmentPanel)
+ {
+ viewSize++;
+ }
+ }
+
+ String title = new String(this.getTitle());
+ if (viewtitle != null)
+ {
+ title = viewtitle + " ( " + title + ")";
+ }
+ else
+ {
+ if (title.indexOf("(View") > -1)
+ {
+ title = title.substring(0, title.indexOf("(View"));
+ }
+ title += "(View " + viewSize + ")";
+ }
+
+ newaf.setTitle(title.toString());
+
+ newaf.viewport.setHistoryList(viewport.getHistoryList());
+ newaf.viewport.setRedoList(viewport.getRedoList());
+ return newaf;
+ }
+
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ /**
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+
+ /**
+ * Change the display state for the given feature groups
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ FeatureRenderer fr = null;
+ this.sequenceFeatures.setState(true);
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.seqPanel.seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ public void seqLimits_itemStateChanged()
+ {
+ viewport.setShowJVSuffix(seqLimits.getState());
+ alignPanel.fontChanged();
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void colourTextMenuItem_actionPerformed()
+ {
+ viewport.setColourText(colourTextMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void displayNonconservedMenuItem_actionPerformed()
+ {
+ viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void wrapMenuItem_actionPerformed()
+ {
+ viewport.setWrapAlignment(wrapMenuItem.getState());
+ alignPanel.setWrapAlignment(wrapMenuItem.getState());
+ scaleAbove.setEnabled(wrapMenuItem.getState());
+ scaleLeft.setEnabled(wrapMenuItem.getState());
+ scaleRight.setEnabled(wrapMenuItem.getState());
+ alignPanel.paintAlignment(true);
+ }
+
+ public void overviewMenuItem_actionPerformed()
+ {
+ if (alignPanel.overviewPanel != null)
+ {
+ return;
+ }
+
+ Frame frame = new Frame();
+ OverviewPanel overview = new OverviewPanel(alignPanel);
+ frame.add(overview);
+ // +50 must allow for applet frame window
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.overview_params", new String[] { this.getTitle() }),
+ overview.getPreferredSize().width,
+ overview.getPreferredSize().height + 50);
+
+ frame.pack();
+ final AlignmentPanel ap = alignPanel;
+ frame.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosing(WindowEvent e)
+ {
+ if (ap != null)
+ {
+ ap.setOverviewPanel(null);
+ }
+ };
+ });
+
+ alignPanel.setOverviewPanel(overview);
+
+ }
+
+ public void changeColour(ColourSchemeI cs)
+ {
+
+ if (cs != null)
+ {
+ if (viewport.getAbovePIDThreshold())
+ {
+ viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
+ cs, "Background"));
+ }
+
+ if (viewport.getConservationSelected())
+ {
+ cs.setConservationApplied(true);
+ viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
+ cs, "Background"));
+ }
+ else
+ {
+ cs.setConservationApplied(false);
+ }
+ }
+ viewport.setGlobalColourScheme(cs);
+
+ alignPanel.paintAlignment(true);
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ if (viewport.getAbovePIDThreshold()
+ && viewport.getGlobalColourScheme() != null)
+ {
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ if (viewport.getConservationSelected()
+ && viewport.getGlobalColourScheme() != null)
+ {
+ SliderPanel.setConservationSlider(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void conservationMenuItem_actionPerformed()
+ {
+ viewport.setConservationSelected(conservationMenuItem.getState());
+
+ viewport.setAbovePIDThreshold(false);
+ abovePIDThreshold.setState(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyConservation_actionPerformed();
+ }
+
+ public void abovePIDThreshold_actionPerformed()
+ {
+ viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
+
+ conservationMenuItem.setState(false);
+ viewport.setConservationSelected(false);
+
+ changeColour(viewport.getGlobalColourScheme());
+
+ modifyPID_actionPerformed();
+ }
+
+ public void sortPairwiseMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
+ .getAlignment().getSequenceAt(0), null);
+
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortIDMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByID(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortLengthMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByLength(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ public void sortGroupMenuItem_actionPerformed()
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByGroup(viewport.getAlignment());
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ public void removeRedundancyMenuItem_actionPerformed()
+ {
+ new RedundancyPanel(alignPanel);
+ }
+
+ public void pairwiseAlignmentMenuItem_actionPerformed()
+ {
+ if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() > 1)
+ {
+ Frame frame = new Frame();
+ frame.add(new PairwiseAlignPanel(alignPanel));
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.pairwise_alignment"), 600,
+ 500);
+ }
+ }
+
+ public void PCAMenuItem_actionPerformed()
+ {
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ SequenceI current;
+ int Width = viewport.getAlignment().getWidth();
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+
+ if (current.getLength() < Width)
+ {
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());
+ }
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ if ((viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() < 4 && viewport
+ .getSelectionGroup().getSize() > 0)
+ || viewport.getAlignment().getHeight() < 4)
+ {
+ return;
+ }
+
+ try
+ {
+ new PCAPanel(viewport);
+ } catch (java.lang.OutOfMemoryError ex)
+ {
+ }
+
+ }
+
+ public void averageDistanceTreeMenuItem_actionPerformed()
+ {
+ NewTreePanel("AV", "PID", "Average distance tree using PID");
+ }
+
+ public void neighbourTreeMenuItem_actionPerformed()
+ {
+ NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ }
+
+ protected void njTreeBlosumMenuItem_actionPerformed()
+ {
+ NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ }
+
+ protected void avTreeBlosumMenuItem_actionPerformed()
+ {
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ }
+
+ void NewTreePanel(String type, String pwType, String title)
+ {
+ // are the sequences aligned?
+ if (!viewport.getAlignment().isAligned(false))
+ {
+ SequenceI current;
+ int Width = viewport.getAlignment().getWidth();
+
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
+ {
+ current = viewport.getAlignment().getSequenceAt(i);
+
+ if (current.getLength() < Width)
+ {
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());
+ }
+ }
+ alignPanel.paintAlignment(true);
+
+ }
+
+ if ((viewport.getSelectionGroup() != null && viewport
+ .getSelectionGroup().getSize() > 1)
+ || (viewport.getAlignment().getHeight() > 1))
+ {
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);
+
+ addTreeMenuItem(tp, title);
+
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+ }
+ }
+
+ void loadTree_actionPerformed()
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
+ cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
+ cap.setTreeImport();
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.paste_newick_file"), 400, 300);
+ }
+
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)
+ {
+ TreePanel tp = new TreePanel(alignPanel, treeFile,
+ MessageManager.getString("label.load_tree_from_file"), tree);
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+ addTreeMenuItem(tp, treeFile);
+ }
+
+ /**
+ * sort the alignment using the given treePanel
+ *
+ * @param treePanel
+ * tree used to sort view
+ * @param title
+ * string used for undo event name
+ */
+ public void sortByTree(TreePanel treePanel, String title)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+ // HistoryItem.SORT));
+ addHistoryItem(new OrderCommand(MessageManager.formatMessage(
+ "label.order_by_params", new String[] { title }), oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ * Do any automatic reordering of the alignment and add the necessary bits to
+ * the menu structure for the new tree
+ *
+ * @param treePanel
+ * @param title
+ */
+ protected void addTreeMenuItem(final TreePanel treePanel,
+ final String title)
+ {
+ final MenuItem item = new MenuItem(title);
+ sortByTreeMenu.add(item);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ sortByTree(treePanel, title); // treePanel.getTitle());
+ }
+ });
+
+ treePanel.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowOpened(WindowEvent e)
+ {
+ if (viewport.sortByTree)
+ {
+ sortByTree(treePanel, title);
+ }
+ super.windowOpened(e);
+ }
+
+ @Override
+ public void windowClosing(WindowEvent e)
+ {
+ sortByTreeMenu.remove(item);
+ };
+ });
+ }
+
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ if (viewport.applet.debug)
+ {
+ System.err.println("Sorting " + alorder.getOrder().size()
+ + " in alignment '" + getTitle() + "'");
+ }
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.getAlignment()));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
+ protected void documentation_actionPerformed()
+ {
+ alignPanel.av.applet.openJalviewHelpUrl();
+ }
+
+ protected void about_actionPerformed()
+ {
+
+ class AboutPanel extends Canvas
+ {
+ String version;
+
+ String builddate;
+
+ public AboutPanel(String version, String builddate)
+ {
+ this.version = version;
+ this.builddate = builddate;
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ FontMetrics fm = g.getFontMetrics();
+ int fh = fm.getHeight();
+ int y = 5, x = 7;
+ g.setColor(Color.black);
+ // TODO: update this text for each release or centrally store it for
+ // lite and application
+ g.setFont(new Font("Helvetica", Font.BOLD, 14));
+ g.drawString(MessageManager.formatMessage(
+ "label.jalviewLite_release", new String[] { version }), x,
+ y += fh);
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));
+ g.drawString(MessageManager.formatMessage(
+ "label.jaview_build_date", new String[] { builddate }), x,
+ y += fh);
+ g.setFont(new Font("Helvetica", Font.PLAIN, 12));
+ g.drawString(MessageManager.getString("label.jalview_authors_1"),
+ x, y += fh * 1.5);
+ g.drawString(MessageManager.getString("label.jalview_authors_2"),
+ x + 50, y += fh + 8);
+ g.drawString(
+ MessageManager.getString("label.jalview_dev_managers"), x,
+ y += fh);
+ g.drawString(MessageManager
+ .getString("label.jalview_distribution_lists"), x, y += fh);
+ g.drawString(MessageManager.getString("label.jalview_please_cite"),
+ x, y += fh + 8);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_authors"),
+ x, y += fh);
+ g.drawString(
+ MessageManager.getString("label.jalview_cite_1_title"), x,
+ y += fh);
+ g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
+ x, y += fh);
+ }
+ }
+
+ Frame frame = new Frame();
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
+ .getBuildDate()));
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.jalview"), 580, 220);
+
+ }
+
+ public void showURL(String url, String target)
+ {
+ if (viewport.applet == null)
+ {
+ System.out.println("Not running as applet - no browser available.");
+ }
+ else
+ {
+ viewport.applet.showURL(url, target);
+ }
+ }
+
+ // ////////////////////////////////////////////////////////////////////////////////
+ // JBuilder Graphics here
+
+ MenuBar alignFrameMenuBar = new MenuBar();
+
+ Menu fileMenu = new Menu(MessageManager.getString("action.file"));
+
+ MenuItem loadApplication = new MenuItem(
+ MessageManager.getString("label.view_full_application"));
+
+ MenuItem loadTree = new MenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+
+ MenuItem loadAnnotations = new MenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+
+ MenuItem outputFeatures = new MenuItem(
+ MessageManager.getString("label.export_features"));
+
+ MenuItem outputAnnotations = new MenuItem(
+ MessageManager.getString("label.export_annotations"));
+
+ MenuItem closeMenuItem = new MenuItem(
+ MessageManager.getString("action.close"));
+
+ MenuItem selectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.select_all"));
+
+ MenuItem deselectAllSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.deselect_all"));
+
+ MenuItem invertSequenceMenuItem = new MenuItem(
+ MessageManager.getString("action.invert_selection"));
+
+ MenuItem remove2LeftMenuItem = new MenuItem();
+
+ MenuItem remove2RightMenuItem = new MenuItem();
+
+ MenuItem removeGappedColumnMenuItem = new MenuItem();
+
+ MenuItem removeAllGapsMenuItem = new MenuItem();
+
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
+
+ MenuItem sortPairwiseMenuItem = new MenuItem();
+
+ MenuItem sortIDMenuItem = new MenuItem();
+
+ MenuItem sortLengthMenuItem = new MenuItem();
+
+ MenuItem sortGroupMenuItem = new MenuItem();
+
+ MenuItem removeRedundancyMenuItem = new MenuItem();
+
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();
+
+ MenuItem PCAMenuItem = new MenuItem();
+
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();
+
+ MenuItem neighbourTreeMenuItem = new MenuItem();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ public Label statusBar = new Label();
+
+ MenuItem clustalColour = new MenuItem();
+
+ MenuItem zappoColour = new MenuItem();
+
+ MenuItem taylorColour = new MenuItem();
+
+ MenuItem hydrophobicityColour = new MenuItem();
+
+ MenuItem helixColour = new MenuItem();
+
+ MenuItem strandColour = new MenuItem();
+
+ MenuItem turnColour = new MenuItem();
+
+ MenuItem buriedColour = new MenuItem();
+
+ MenuItem purinePyrimidineColour = new MenuItem();
+
+ // MenuItem RNAInteractionColour = new MenuItem();
+
+ MenuItem RNAHelixColour = new MenuItem();
+
+ MenuItem userDefinedColour = new MenuItem();
+
+ MenuItem PIDColour = new MenuItem();
+
+ MenuItem BLOSUM62Colour = new MenuItem();
+
+ MenuItem tcoffeeColour = new MenuItem();
+
+ MenuItem njTreeBlosumMenuItem = new MenuItem();
+
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
+
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
+
+ MenuItem alProperties = new MenuItem(
+ MessageManager.getString("label.alignment_props"));
+
+ MenuItem overviewMenuItem = new MenuItem();
+
+ MenuItem undoMenuItem = new MenuItem();
+
+ MenuItem redoMenuItem = new MenuItem();
+
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
+
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
+
+ MenuItem findMenuItem = new MenuItem();
+
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
+
+ MenuItem nucleotideColour = new MenuItem();
+
+ MenuItem deleteGroups = new MenuItem();
+
+ MenuItem grpsFromSelection = new MenuItem();
+
+ MenuItem createGroup = new MenuItem();
+
+ MenuItem unGroup = new MenuItem();
+
+ MenuItem delete = new MenuItem();
+
+ MenuItem copy = new MenuItem();
+
+ MenuItem cut = new MenuItem();
+
+ Menu pasteMenu = new Menu();
+
+ MenuItem pasteNew = new MenuItem();
+
+ MenuItem pasteThis = new MenuItem();
+
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
+
+ MenuItem font = new MenuItem();
+
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
+
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();
+
+ MenuItem modifyPID = new MenuItem();
+
+ MenuItem modifyConservation = new MenuItem();
+
+ CheckboxMenuItem autoCalculate = null;
+
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+ "Sort Alignment With New Tree", true);
+
+ Menu sortByTreeMenu = new Menu();
+
+ MenuItem inputText = new MenuItem();
+
+ MenuItem documentation = new MenuItem();
+
+ MenuItem about = new MenuItem();
+
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();
+
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
+
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
+
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
+
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
+
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
+
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
+
+ /**
+ * Initialise menus and other items
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ setMenuBar(alignFrameMenuBar);
+
+ /*
+ * Configure File menu items and actions
+ */
+ inputText
+ .setLabel(MessageManager.getString("label.input_from_textbox"));
+ inputText.addActionListener(this);
+ Menu outputTextboxMenu = new Menu(
+ MessageManager.getString("label.out_to_textbox"));
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+
+ MenuItem item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputTextboxMenu.add(item);
+ }
+ closeMenuItem.addActionListener(this);
+ loadApplication.addActionListener(this);
+ loadTree.addActionListener(this);
+ loadAnnotations.addActionListener(this);
+ outputFeatures.addActionListener(this);
+ outputAnnotations.addActionListener(this);
+
+ /*
+ * Configure Edit menu items and actions
+ */
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setLabel(MessageManager.getString("action.undo"));
+ undoMenuItem.addActionListener(this);
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setLabel(MessageManager.getString("action.redo"));
+ redoMenuItem.addActionListener(this);
+ copy.setLabel(MessageManager.getString("action.copy"));
+ copy.addActionListener(this);
+ cut.setLabel(MessageManager.getString("action.cut"));
+ cut.addActionListener(this);
+ delete.setLabel(MessageManager.getString("action.delete"));
+ delete.addActionListener(this);
+ pasteMenu.setLabel(MessageManager.getString("action.paste"));
+ pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
+ pasteNew.addActionListener(this);
+ pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
+ pasteThis.addActionListener(this);
+ remove2LeftMenuItem.setLabel(MessageManager
+ .getString("action.remove_left"));
+ remove2LeftMenuItem.addActionListener(this);
+ remove2RightMenuItem.setLabel(MessageManager
+ .getString("action.remove_right"));
+ remove2RightMenuItem.addActionListener(this);
+ removeGappedColumnMenuItem.setLabel(MessageManager
+ .getString("action.remove_empty_columns"));
+ removeGappedColumnMenuItem.addActionListener(this);
+ removeAllGapsMenuItem.setLabel(MessageManager
+ .getString("action.remove_all_gaps"));
+ removeAllGapsMenuItem.addActionListener(this);
+ removeRedundancyMenuItem.setLabel(MessageManager
+ .getString("action.remove_redundancy"));
+ removeRedundancyMenuItem.addActionListener(this);
+
+ /*
+ * Configure Select menu items and actions
+ */
+ findMenuItem.setLabel(MessageManager.getString("action.find"));
+ findMenuItem.addActionListener(this);
+ selectAllSequenceMenuItem.addActionListener(this);
+ deselectAllSequenceMenuItem.addActionListener(this);
+ invertSequenceMenuItem.setLabel(MessageManager
+ .getString("action.invert_sequence_selection"));
+ invertSequenceMenuItem.addActionListener(this);
+ invertColSel.setLabel(MessageManager
+ .getString("action.invert_column_selection"));
+ invertColSel.addActionListener(this);
+ deleteGroups.setLabel(MessageManager
+ .getString("action.undefine_groups"));
+ deleteGroups.addActionListener(this);
+ grpsFromSelection.setLabel(MessageManager
+ .getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(this);
+ createGroup.setLabel(MessageManager.getString("action.create_group"));
+ unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ annotationColumnSelection.setLabel(MessageManager
+ .getString("action.select_by_annotation"));
+ annotationColumnSelection.addActionListener(this);
+
+ /*
+ * Configure View menu items and actions
+ */
+ newView.setLabel(MessageManager.getString("action.new_view"));
+ newView.addActionListener(this);
+ Menu showMenu = new Menu(MessageManager.getString("action.show"));
+ showColumns.setLabel(MessageManager.getString("label.all_columns"));
+ showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
+ Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
+ hideColumns
+ .setLabel(MessageManager.getString("label.selected_columns"));
+ hideSequences.setLabel(MessageManager
+ .getString("label.selected_sequences"));
+ hideAllButSelection.setLabel(MessageManager
+ .getString("label.all_but_selected_region"));
+ hideAllSelection.setLabel(MessageManager
+ .getString("label.selected_region"));
+ showAllHidden.setLabel(MessageManager
+ .getString("label.all_sequences_columns"));
+ showColumns.addActionListener(this);
+ showSeqs.addActionListener(this);
+ hideColumns.addActionListener(this);
+ hideSequences.addActionListener(this);
+ hideAllButSelection.addActionListener(this);
+ hideAllSelection.addActionListener(this);
+ showAllHidden.addActionListener(this);
+ featureSettings.setLabel(MessageManager
+ .getString("action.feature_settings"));
+ featureSettings.addActionListener(this);
+ sequenceFeatures.setLabel(MessageManager
+ .getString("label.show_sequence_features"));
+ sequenceFeatures.addItemListener(this);
+ sequenceFeatures.setState(false);
+ followMouseOverFlag.setLabel(MessageManager
+ .getString("label.automatic_scrolling"));
+ followMouseOverFlag.addItemListener(this);
+ alProperties.addActionListener(this);
+ overviewMenuItem.setLabel(MessageManager
+ .getString("label.overview_window"));
+ overviewMenuItem.addActionListener(this);
+
+ /*
+ * Configure Annotations menu items and actions
+ */
+ annotationPanelMenuItem.setLabel(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.addItemListener(this);
+ showGroupConsensus.setLabel(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConservation.setLabel(MessageManager
+ .getString("label.group_conservation"));
+ showConsensusHistogram.setLabel(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showSequenceLogo.setLabel(MessageManager
+ .getString("label.show_consensus_logo"));
+ normSequenceLogo.setLabel(MessageManager
+ .getString("label.norm_consensus_logo"));
+ applyAutoAnnotationSettings.setLabel(MessageManager
+ .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setState(true);
+ Menu autoAnnMenu = new Menu(
+ MessageManager.getString("label.autocalculated_annotation"));
+ showGroupConsensus.addItemListener(this);
+ showGroupConservation.addItemListener(this);
+ showConsensusHistogram.addItemListener(this);
+ showSequenceLogo.addItemListener(this);
+ normSequenceLogo.addItemListener(this);
+ applyAutoAnnotationSettings.addItemListener(this);
+ showAlignmentAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_al_annotations"));
+ showSequenceAnnotations = new CheckboxMenuItem(
+ MessageManager.getString("label.show_all_seq_annotations"));
+ sortAnnBySequence = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ sortAnnByLabel = new CheckboxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+ showAutoFirst = new CheckboxMenuItem(
+ MessageManager.getString("label.show_first"));
+ showAutoLast = new CheckboxMenuItem(
+ MessageManager.getString("label.show_last"));
+ showAlignmentAnnotations.addItemListener(this);
+ showSequenceAnnotations.addItemListener(this);
+ sortAnnBySequence.addItemListener(this);
+ sortAnnByLabel.addItemListener(this);
+ showAutoFirst.addItemListener(this);
+ showAutoLast.addItemListener(this);
+
+ /*
+ * Configure Format menu items and actions
+ */
+ font.setLabel(MessageManager.getString("action.font"));
+ font.addActionListener(this);
+ scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
+ scaleAbove.setState(true);
+ scaleAbove.setEnabled(false);
+ scaleAbove.addItemListener(this);
+ scaleLeft.setEnabled(false);
+ scaleLeft.setState(true);
+ scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
+ scaleLeft.addItemListener(this);
+ scaleRight.setEnabled(false);
+ scaleRight.setState(true);
+ scaleRight.setLabel(MessageManager.getString("action.scale_right"));
+ scaleRight.addItemListener(this);
+ viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addItemListener(this);
+ viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addItemListener(this);
+ colourTextMenuItem.setLabel(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addItemListener(this);
+ displayNonconservedMenuItem.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconservedMenuItem.addItemListener(this);
+ wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
+ wrapMenuItem.addItemListener(this);
+ renderGapsMenuItem.setLabel(MessageManager
+ .getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addItemListener(this);
+ centreColumnLabelFlag.setLabel(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelFlag.addItemListener(this);
+ seqLimits.setState(true);
+ seqLimits.setLabel(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.addItemListener(this);
+
+ /*
+ * Configure Colour menu items and actions
+ */
+ applyToAllGroups.setLabel(MessageManager
+ .getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.setState(true);
+ applyToAllGroups.addItemListener(this);
+ clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(this);
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(this);
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(this);
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(this);
+ // RNAInteractionColour.setLabel(MessageManager
+ // .getString("label.rna_interaction"));
+ // RNAInteractionColour.addActionListener(this);
+ RNAHelixColour.setLabel(MessageManager
+ .getString("action.by_rna_helixes"));
+ RNAHelixColour.addActionListener(this);
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(this);
+ tcoffeeColour
+ .setLabel(MessageManager.getString("label.tcoffee_scores"));
+ // it will be enabled only if a score file is provided
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(this);
+ conservationMenuItem.setLabel(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addItemListener(this);
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(this);
+ abovePIDThreshold.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addItemListener(this);
+ nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_thereshold"));
+ modifyPID.addActionListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_thereshold"));
+ modifyConservation.addActionListener(this);
+ annotationColour.setLabel(MessageManager
+ .getString("action.by_annotation"));
+ annotationColour.addActionListener(this);
+
+ /*
+ * Configure Calculate menu items and actions
+ */
+ sortPairwiseMenuItem.setLabel(MessageManager
+ .getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(this);
+ sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(this);
+ sortLengthMenuItem.setLabel(MessageManager
+ .getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(this);
+ sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(this);
+ pairwiseAlignmentMenuItem.setLabel(MessageManager
+ .getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(this);
+ PCAMenuItem.setLabel(MessageManager
+ .getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(this);
+ autoCalculate = new CheckboxMenuItem(
+ MessageManager.getString("label.autocalculate_consensus"), true);
+ averageDistanceTreeMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(this);
+ neighbourTreeMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(this);
+ avDistanceTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.average_distance_bloslum62"));
+ avDistanceTreeBlosumMenuItem.addActionListener(this);
+ njTreeBlosumMenuItem.setLabel(MessageManager
+ .getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(this);
+ sortByTreeMenu.setLabel(MessageManager
+ .getString("action.by_tree_order"));
+ Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
+ Menu calculateTreeMenu = new Menu(
+ MessageManager.getString("action.calculate_tree"));
+ autoCalculate.addItemListener(this);
+ sortByTree.addItemListener(this);
+
+ /*
+ * Configure Help menu items and actions
+ */
+ Menu helpMenu = new Menu(MessageManager.getString("action.help"));
+ documentation.setLabel(MessageManager.getString("label.documentation"));
+ documentation.addActionListener(this);
+ about.setLabel(MessageManager.getString("label.about"));
+ about.addActionListener(this);
+
+ /*
+ * Add top level menus to frame
+ */
+ alignFrameMenuBar.add(fileMenu);
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
+ alignFrameMenuBar.add(editMenu);
+ Menu selectMenu = new Menu(MessageManager.getString("action.select"));
+ alignFrameMenuBar.add(selectMenu);
+ Menu viewMenu = new Menu(MessageManager.getString("action.view"));
+ alignFrameMenuBar.add(viewMenu);
+ Menu annotationsMenu = new Menu(
+ MessageManager.getString("action.annotations"));
+ alignFrameMenuBar.add(annotationsMenu);
+ Menu formatMenu = new Menu(MessageManager.getString("action.format"));
+ alignFrameMenuBar.add(formatMenu);
+ Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
+ alignFrameMenuBar.add(colourMenu);
+ Menu calculateMenu = new Menu(
+ MessageManager.getString("action.calculate"));
+ alignFrameMenuBar.add(calculateMenu);
+ alignFrameMenuBar.add(helpMenu);
+
+ /*
+ * File menu
+ */
+ 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);
+
+ /*
+ * Edit menu
+ */
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
+ editMenu.addSeparator();
+ editMenu.add(remove2LeftMenuItem);
+ editMenu.add(remove2RightMenuItem);
+ editMenu.add(removeGappedColumnMenuItem);
+ editMenu.add(removeAllGapsMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+
+ /*
+ * Select menu
+ */
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumnSelection);
+
+ /*
+ * View menu
+ */
+ viewMenu.add(newView);
+ viewMenu.addSeparator();
+ showMenu.add(showColumns);
+ showMenu.add(showSeqs);
+ showMenu.add(showAllHidden);
+ viewMenu.add(showMenu);
+ hideMenu.add(hideColumns);
+ hideMenu.add(hideSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
+ viewMenu.add(hideMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(followMouseOverFlag);
+ viewMenu.addSeparator();
+ viewMenu.add(sequenceFeatures);
+ viewMenu.add(featureSettings);
+ viewMenu.addSeparator();
+ viewMenu.add(alProperties);
+ viewMenu.addSeparator();
+ viewMenu.add(overviewMenuItem);
+
+ /*
+ * Annotations menu
+ */
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAlignmentAnnotations);
+ annotationsMenu.add(showSequenceAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ annotationsMenu.add(autoAnnMenu);
+
+ /*
+ * Format menu
+ */
+ formatMenu.add(font);
+ formatMenu.add(seqLimits);
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(displayNonconservedMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelFlag);
+
+ /*
+ * Colour menu
+ */
+ 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(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(tcoffeeColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+ colourMenu.add(RNAHelixColour);
+
+ /*
+ * Calculate menu
+ */
+ sortMenu.add(sortIDMenuItem);
+ sortMenu.add(sortLengthMenuItem);
+ sortMenu.add(sortByTreeMenu);
+ sortMenu.add(sortGroupMenuItem);
+ sortMenu.add(sortPairwiseMenuItem);
+ calculateMenu.add(sortMenu);
+ calculateTreeMenu.add(averageDistanceTreeMenuItem);
+ calculateTreeMenu.add(neighbourTreeMenuItem);
+ calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
+ calculateTreeMenu.add(njTreeBlosumMenuItem);
+ calculateMenu.add(calculateTreeMenu);
+ calculateMenu.addSeparator();
+ calculateMenu.add(pairwiseAlignmentMenuItem);
+ calculateMenu.add(PCAMenuItem);
+ calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
+
+ /*
+ * Help menu
+ */
+ helpMenu.add(documentation);
+ helpMenu.add(about);
+
+ /*
+ * Status bar
+ */
+ statusBar.setBackground(Color.white);
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ this.add(statusBar, BorderLayout.SOUTH);
+ }
+
+ public void setStatus(String string)
+ {
+ statusBar.setText(string);
+ };
+
+ MenuItem featureSettings = new MenuItem();
+
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
+
+ MenuItem annotationColour = new MenuItem();
+
+ MenuItem annotationColumnSelection = new MenuItem();
+
+ MenuItem invertColSel = new MenuItem();
+
+ MenuItem showColumns = new MenuItem();
+
+ MenuItem showSeqs = new MenuItem();
+
+ MenuItem hideColumns = new MenuItem();
+
+ MenuItem hideSequences = new MenuItem();
+
+ MenuItem hideAllButSelection = new MenuItem();
+
+ MenuItem hideAllSelection = new MenuItem();
+
+ MenuItem showAllHidden = new MenuItem();
+
+ MenuItem newView = new MenuItem();
+
+ private CheckboxMenuItem showAlignmentAnnotations;
+
+ private CheckboxMenuItem showSequenceAnnotations;
+
+ private CheckboxMenuItem sortAnnBySequence;
+
+ private CheckboxMenuItem sortAnnByLabel;
+
+ private CheckboxMenuItem showAutoFirst;
+
+ private CheckboxMenuItem showAutoLast;
+
+ private SplitFrame splitFrame;
+
+ /**
+ * Attach the alignFrame panels after embedding menus, if necessary. This used
+ * to be called setEmbedded, but is now creates the dropdown menus in a
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.
+ *
+ * @param reallyEmbedded
+ * true to attach the view to the applet area on the page rather than
+ * in a new window
+ */
+ public void createAlignFrameWindow(boolean reallyEmbedded)
+ {
+ if (reallyEmbedded)
+ {
+ embedAlignFrameInApplet(viewport.applet);
+ }
+ else
+ {
+ // //////
+ // test and embed menu bar if necessary.
+ //
+ if (embedMenuIfNeeded(alignPanel))
+ {
+ /*
+ * adjust for status bar height too. ? pointless as overridden by layout
+ * manager
+ */
+ alignPanel.setSize(getSize().width,
+ getSize().height - statusBar.getHeight());
+ }
+ add(statusBar, BorderLayout.SOUTH);
+ add(alignPanel, BorderLayout.CENTER);
+ // and register with the applet so it can pass external API calls to us
+ jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
+ frameHeight);
+ }
+ }
+
+ /**
+ * Add the components of this AlignFrame to the applet container.
+ *
+ * @param theApplet
+ */
+ public void embedAlignFrameInApplet(final JalviewLite theApplet)
+ {
+ // ////
+ // Explicitly build the embedded menu panel for the on-page applet
+ //
+ // view cannot be closed if its actually on the page
+ fileMenu.remove(closeMenuItem);
+ fileMenu.remove(3); // Remove Separator
+ // construct embedded menu, using default font
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
+ // and actually add the components to the applet area
+ theApplet.setLayout(new BorderLayout());
+ theApplet.add(embeddedMenu, BorderLayout.NORTH);
+ theApplet.add(statusBar, BorderLayout.SOUTH);
+ // TODO should size be left to the layout manager?
+ alignPanel.setSize(theApplet.getSize().width,
+ theApplet.getSize().height - embeddedMenu.getHeight()
+ - statusBar.getHeight());
+ theApplet.add(alignPanel, BorderLayout.CENTER);
+ final AlignFrame me = this;
+ theApplet.addFocusListener(new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ if (theApplet.currentAlignFrame == me)
+ {
+ theApplet.currentAlignFrame = null;
+ }
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ theApplet.currentAlignFrame = me;
+ }
+ });
+ theApplet.validate();
+ }
+
+ /**
+ * create a new binding between structures in an existing jmol viewer instance
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,
+ * this does not open a new Jmol window, or modify the display of the
+ * structures in the original jmol window. Note This method doesn't work
+ * without an additional javascript library to exchange messages between the
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621
+ *
+ * @param viewer
+ * JmolViewer instance
+ * @param sequenceIds
+ * - sequence Ids to search for associations
+ */
+ public SequenceStructureBinding addStructureViewInstance(
+ Object jmolviewer, String[] sequenceIds)
+ {
+ Viewer viewer = null;
+ try
+ {
+ viewer = (Viewer) jmolviewer;
+ } catch (ClassCastException ex)
+ {
+ System.err.println("Unsupported viewer object :"
+ + jmolviewer.getClass());
+ }
+ if (viewer == null)
+ {
+ System.err.println("Can't use this object as a structure viewer:"
+ + jmolviewer.getClass());
+ return null;
+ }
+ SequenceI[] seqs = null;
+ if (sequenceIds == null || sequenceIds.length == 0)
+ {
+ seqs = viewport.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ Vector sqi = new Vector();
+ AlignmentI al = viewport.getAlignment();
+ for (int sid = 0; sid < sequenceIds.length; sid++)
+ {
+ SequenceI sq = al.findName(sequenceIds[sid]);
+ if (sq != null)
+ {
+ sqi.addElement(sq);
+ }
+ }
+ if (sqi.size() > 0)
+ {
+ seqs = new SequenceI[sqi.size()];
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
+ {
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);
+ }
+ }
+ else
+ {
+ return null;
+ }
+ }
+ AAStructureBindingModel jmv = null;
+ // TODO: search for a jmv that involves viewer
+ if (jmv == null)
+ { // create a new viewer/jalview binding.
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
+ }
+ return jmv;
+
+ }
+
+ /**
+ * bind a pdb file to a sequence in the current view
+ *
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
+ */
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,
+ String pdbFile)
+ {
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
+ {
+ Vector pdbe = toaddpdb.getAllPDBEntries();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
+ {
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
+ {
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
+ {
+ pdbentry = null;
+ }
+ else
+ {
+ continue;
+ }
+ }
+ }
+ if (pdbentry == null)
+ {
+ pdbentry = new PDBEntry();
+ pdbentry.setId(pdbEntryString);
+ pdbentry.setFile(pdbFile);
+ needtoadd = true; // add this new entry to sequence.
+ }
+ // resolve data source
+ // TODO: this code should be a refactored to an io package
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+ if (protocol == null)
+ {
+ return false;
+ }
+ if (needtoadd)
+ {
+ // make a note of the access mode and add
+ if (pdbentry.getProperty() == null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ }
+ pdbentry.getProperty().put("protocol", protocol);
+ toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
+ }
+ }
+ return true;
+ }
+
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
+ {
+ if (seqs != null)
+ {
+ Vector sequences = new Vector();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ sequences.addElement(new Object[] { seqs[i],
+ (chains != null) ? chains[i] : null });
+ }
+ }
+ seqs = new SequenceI[sequences.size()];
+ chains = new String[sequences.size()];
+ for (int i = 0, isize = sequences.size(); i < isize; i++)
+ {
+ Object[] oj = (Object[]) sequences.elementAt(i);
+
+ seqs[i] = (SequenceI) oj[0];
+ chains[i] = (String) oj[1];
+ }
+ }
+ return new Object[] { seqs, chains };
+
+ }
+
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, String protocol)
+ {
+ // Scrub any null sequences from the array
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);
+ seqs = (SequenceI[]) sqch[0];
+ chains = (String[]) sqch[1];
+ if (seqs == null || seqs.length == 0)
+ {
+ System.err
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
+ }
+ if (protocol == null || protocol.trim().length() == 0
+ || protocol.equals("null"))
+ {
+ protocol = (String) pdb.getProperty().get("protocol");
+ if (protocol == null)
+ {
+ System.err.println("Couldn't work out protocol to open structure: "
+ + pdb.getId());
+ return;
+ }
+ }
+ if (applet.useXtrnalSviewer)
+ {
+ // register the association(s) and quit, don't create any windows.
+ if (StructureSelectionManager.getStructureSelectionManager(applet)
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ {
+ System.err.println("Failed to map " + pdb.getFile() + " ("
+ + protocol + ") to any sequences");
+ }
+ return;
+ }
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)
+ {
+ // can only do alignments with Jmol
+ // find the last jmol window assigned to this alignment
+ jalview.appletgui.AppletJmol ajm = null, tajm;
+ Vector jmols = applet
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)
+ {
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+ if (tajm.ap.alignFrame == this)
+ {
+ ajm = tajm;
+ break;
+ }
+ }
+ if (ajm != null)
+ {
+ System.err
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ // try and add the pdb structure
+ // ajm.addS
+ ajm = null;
+ }
+ }
+ // otherwise, create a new window
+ if (applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+ protocol);
+ applet.lastFrameX += 40;
+ applet.lastFrameY += 40;
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+ }
+
+ }
+
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
+ SequenceI[][] seqs, String[][] chains, String[] protocols)
+ {
+ // TODO Auto-generated method stub
+ System.err.println("Aligned Structure View: Not yet implemented.");
+ }
+
+ /**
+ * modify the current selection, providing the user has not made a selection
+ * already.
+ *
+ * @param sel
+ * - sequences from this alignment
+ * @param csel
+ * - columns to be selected on the alignment
+ */
+ public void select(SequenceGroup sel, ColumnSelection csel)
+ {
+ alignPanel.seqPanel.selection(sel, csel, null);
+ }
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.seqPanel.scrollTo(row, column);
+ }
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.seqPanel.scrollToRow(row);
+ }
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.seqPanel.scrollToColumn(column);
+ }
+
+ /**
+ * @return the alignments unique ID.
+ */
+ public String getSequenceSetId()
+ {
+ return viewport.getSequenceSetId();
+ }
+
+ /**
+ * Load the (T-Coffee) score file from the specified url
+ *
+ * @param source
+ * File/URL/T-COFFEE score file contents
+ * @throws IOException
+ * @return true if alignment was annotated with data from source
+ */
+ public boolean loadScoreFile(String source) throws IOException
+ {
+
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,
+ AppletFormatAdapter.checkProtocol(source));
+ if (!file.isValid())
+ {
+ // TODO: raise dialog for gui
+ System.err.println("Problems parsing T-Coffee scores: "
+ + file.getWarningMessage());
+ System.err.println("Origin was:\n" + source);
+ return false;
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if ((aln = viewport.getAlignment()) != null
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
+ .getWidth()))
+ {
+ // TODO: raise a dialog box here rather than bomb out.
+ System.err
+ .println("The scores matrix does not match the alignment dimensions");
+
+ }
+
+ // TODO add parameter to indicate if matching should be done
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))
+ {
+ alignPanel.fontChanged();
+ tcoffeeColour.setEnabled(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ return true;
+ }
+ else
+ {
+ System.err.println("Problems resolving T-Coffee scores:");
+ if (file.getWarningMessage() != null)
+ {
+ System.err.println(file.getWarningMessage());
+ }
+ }
+ return false;
+ }
+
+ public SplitFrame getSplitFrame()
+ {
+ return this.splitFrame;
+ }
+
+ public void setSplitFrame(SplitFrame sf)
+ {
+ this.splitFrame = sf;
+ }
+
+ // may not need this
+ @Override
+ public void setShowSeqFeatures(boolean b)
+ {
+ // showSeqFeatures.setSelected(b);
+ viewport.setShowSequenceFeatures(b);
+
+ }
+
+ @Override
+ public void setMenusForViewport()
+ {
+ // setMenusFromViewport(viewport);
+
+ }
+
+ @Override
+ public void refreshFeatureUI(boolean enableIfNecessary)
+ {
+ if (enableIfNecessary)
+ {
+ sequenceFeatures.setState(true);
+ alignPanel.av.setShowSequenceFeatures(true);
+ }
+ }
+
+ @Override
+ public FeatureSettingsControllerI getFeatureSettingsUI()
+ {
+ return alignPanel.av.featureSettings;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff