-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- */
-package jalview.appletgui;
-
-import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.JalviewLite;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-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.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.ResidueProperties;
-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 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.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
-{
- public AlignmentPanel alignPanel;
-
- public AlignViewport viewport;
-
- int DEFAULT_WIDTH = 700;
-
- int DEFAULT_HEIGHT = 500;
-
- String jalviewServletURL;
-
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
- String title, boolean embedded)
- {
- if (applet != null)
- {
- jalviewServletURL = applet.getParameter("APPLICATION_URL");
- }
-
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- viewport = new AlignViewport(al, applet);
- alignPanel = new AlignmentPanel(this, viewport);
-
- viewport.updateConservation(alignPanel);
- viewport.updateConsensus(alignPanel);
-
- annotationPanelMenuItem.setState(viewport.showAnnotation);
- displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
- followMouseOverFlag.setState(viewport.getFollowHighlight());
- showGroupConsensus.setState(viewport.isShowGroupConsensus());
- showGroupConservation.setState(viewport.isShowGroupConservation());
- showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
- showSequenceLogo.setState(viewport.isShowSequenceLogo());
- normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
-
- seqLimits.setState(viewport.showJVSuffix);
-
- if (applet != null)
- {
- String param = applet.getParameter("sortBy");
- if (param != null)
- {
- if (param.equalsIgnoreCase("Id"))
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Pairwise Identity"))
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (param.equalsIgnoreCase("Length"))
- {
- sortLengthMenuItem_actionPerformed();
- }
- }
-
- param = applet.getParameter("wrap");
- if (param != null)
- {
- if (param.equalsIgnoreCase("true"))
- {
- wrapMenuItem.setState(true);
- wrapMenuItem_actionPerformed();
- }
- }
- param = applet.getParameter("centrecolumnlabels");
- if (param != null)
- {
- centreColumnLabelFlag.setState(true);
- centreColumnLabelFlag_stateChanged();
- }
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
-
- }
- 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);
- createAlignFrameWindow(embedded, title);
-
- 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().featureColours, featureLinks,
- true, viewport.applet.getDefaultParameter(
- "relaxedidmatch", false));
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- if (featuresFile)
- {
- if (featureLinks.size() > 0)
- {
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
- }
- if (autoenabledisplay)
- {
- viewport.showSequenceFeatures = true;
- sequenceFeatures.setState(true);
- }
- if (viewport.featureSettings != null)
- {
- viewport.featureSettings.refreshTable();
- }
- alignPanel.paintAlignment(true);
- statusBar.setText("Successfully added features to 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("Keyboard editing mode is "
- + (viewport.cursorMode ? "on" : "off"));
- if (viewport.cursorMode)
- {
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
- }
- break;
-
- case KeyEvent.VK_F:
- if (evt.isControlDown())
- {
- findMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_H:
- {
- boolean toggleSeqs = !evt.isControlDown();
- boolean toggleCols = !evt.isShiftDown();
- toggleHiddenRegions(toggleSeqs, toggleCols);
- break;
- }
-
- case KeyEvent.VK_PAGE_UP:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(true);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- - viewport.endSeq + viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_PAGE_DOWN:
- if (viewport.wrapAlignment)
- {
- alignPanel.scrollUp(false);
- }
- else
- {
- alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
- + viewport.endSeq - viewport.startSeq);
- }
- break;
-
- case KeyEvent.VK_Z:
- if (evt.isControlDown())
- {
- undoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_Y:
- if (evt.isControlDown())
- {
- redoMenuItem_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_L:
- if (evt.isControlDown())
- {
- trimAlignment(true);
- }
- break;
-
- case KeyEvent.VK_R:
- if (evt.isControlDown())
- {
- trimAlignment(false);
- }
- break;
-
- case KeyEvent.VK_E:
- if (evt.isControlDown())
- {
- if (evt.isShiftDown())
- {
- this.removeAllGapsMenuItem_actionPerformed();
- }
- else
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- }
- break;
- case KeyEvent.VK_I:
- if (evt.isControlDown())
- {
- if (evt.isAltDown())
- {
- invertColSel_actionPerformed();
- }
- else
- {
- invertSequenceMenuItem_actionPerformed();
- }
- }
- break;
-
- case KeyEvent.VK_U:
- if (evt.isControlDown())
- {
- this.deleteGroups_actionPerformed();
- }
- break;
-
- case KeyEvent.VK_T:
- if (evt.isControlDown())
- {
- newView(null);
- }
- break;
-
- }
- alignPanel.paintAlignment(true);
- }
-
- /**
- * called by key handler and the hide all/show all menu items
- *
- * @param toggleSeqs
- * @param toggleCols
- */
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
- {
- boolean hide = false;
- SequenceGroup sg = viewport.getSelectionGroup();
- if (!toggleSeqs && !toggleCols)
- {
- // Hide everything by the current selection - this is a hack - we do the
- // invert and then hide
- // first check that there will be visible columns after the invert.
- if ((viewport.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)
- {
- if (evt.getSource() == displayNonconservedMenuItem)
- {
- displayNonconservedMenuItem_actionPerformed();
- }
- else if (evt.getSource() == colourTextMenuItem)
- {
- colourTextMenuItem_actionPerformed();
- }
- else if (evt.getSource() == wrapMenuItem)
- {
- wrapMenuItem_actionPerformed();
- }
- else if (evt.getSource() == scaleAbove)
- {
- viewport.setScaleAboveWrapped(scaleAbove.getState());
- }
- else if (evt.getSource() == scaleLeft)
- {
- viewport.setScaleLeftWrapped(scaleLeft.getState());
- }
- else if (evt.getSource() == scaleRight)
- {
- viewport.setScaleRightWrapped(scaleRight.getState());
- }
- else if (evt.getSource() == seqLimits)
- {
- seqLimits_itemStateChanged();
- }
- else if (evt.getSource() == viewBoxesMenuItem)
- {
- viewport.setShowBoxes(viewBoxesMenuItem.getState());
- }
- else if (evt.getSource() == viewTextMenuItem)
- {
- viewport.setShowText(viewTextMenuItem.getState());
- }
- else if (evt.getSource() == renderGapsMenuItem)
- {
- viewport.setRenderGaps(renderGapsMenuItem.getState());
- }
- else if (evt.getSource() == annotationPanelMenuItem)
- {
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
- }
- else if (evt.getSource() == sequenceFeatures)
- {
- viewport.showSequenceFeatures(sequenceFeatures.getState());
- alignPanel.seqPanel.seqCanvas.repaint();
- }
- else if (evt.getSource() == conservationMenuItem)
- {
- conservationMenuItem_actionPerformed();
- }
- else if (evt.getSource() == abovePIDThreshold)
- {
- abovePIDThreshold_actionPerformed();
- }
- else if (evt.getSource() == applyToAllGroups)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
- }
- else if (evt.getSource() == autoCalculate)
- {
- viewport.autoCalculateConsensus = autoCalculate.getState();
- }
- else if (evt.getSource() == sortByTree)
- {
- viewport.sortByTree = sortByTree.getState();
- }
- else if (evt.getSource() == this.centreColumnLabelFlag)
- {
- centreColumnLabelFlag_stateChanged();
- }
- else if (evt.getSource() == this.followMouseOverFlag)
- {
- mouseOverFlag_stateChanged();
- }
- else if (evt.getSource() == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (evt.getSource() == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (evt.getSource() == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (evt.getSource() == normSequenceLogo)
- {
- normSequenceLogo_actionPerformed();
- }
- else if (evt.getSource() == showConsensusHistogram)
- {
- showConsensusHistogram_actionPerformed();
- }
- else if (evt.getSource() == applyAutoAnnotationSettings)
- {
- applyAutoAnnotationSettings_actionPerformed();
- }
- alignPanel.paintAlignment(true);
- }
-
- private void mouseOverFlag_stateChanged()
- {
- viewport.followHighlight = followMouseOverFlag.getState();
- // TODO: could kick the scrollTo mechanism to reset view for current
- // searchresults.
- }
-
- private void centreColumnLabelFlag_stateChanged()
- {
- viewport.centreColumnLabels = centreColumnLabelFlag.getState();
- this.alignPanel.annotationPanel.repaint();
- }
-
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
-
- if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == loadTree)
- {
- loadTree_actionPerformed();
- }
- else if (source == loadApplication)
- {
- launchFullApplication();
- }
- else if (source == loadAnnotations)
- {
- loadAnnotations();
- }
- else if (source == outputAnnotations)
- {
- outputAnnotations(true);
- }
- else if (source == outputFeatures)
- {
- outputFeatures(true, "Jalview");
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == inputText)
- {
- inputText_actionPerformed();
- }
- else if (source == closeMenuItem)
- {
- closeMenuItem_actionPerformed();
- }
- else if (source == undoMenuItem)
- {
- undoMenuItem_actionPerformed();
- }
- else if (source == redoMenuItem)
- {
- redoMenuItem_actionPerformed();
- }
- else if (source == copy)
- {
- copy_actionPerformed();
- }
- else if (source == pasteNew)
- {
- pasteNew_actionPerformed();
- }
- else if (source == pasteThis)
- {
- pasteThis_actionPerformed();
- }
- else if (source == cut)
- {
- cut_actionPerformed();
- }
- else if (source == delete)
- {
- delete_actionPerformed();
- }
- else if (source == grpsFromSelection)
- {
- makeGrpsFromSelection_actionPerformed();
- }
- else if (source == deleteGroups)
- {
- deleteGroups_actionPerformed();
- }
- else if (source == selectAllSequenceMenuItem)
- {
- selectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == deselectAllSequenceMenuItem)
- {
- deselectAllSequenceMenuItem_actionPerformed();
- }
- else if (source == invertSequenceMenuItem)
- {
- invertSequenceMenuItem_actionPerformed();
- }
- else if (source == invertColSel)
- {
- viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
- }
- else if (source == remove2LeftMenuItem)
- {
- trimAlignment(true);
- }
- else if (source == remove2RightMenuItem)
- {
- trimAlignment(false);
- }
- else if (source == removeGappedColumnMenuItem)
- {
- removeGappedColumnMenuItem_actionPerformed();
- }
- else if (source == removeAllGapsMenuItem)
- {
- removeAllGapsMenuItem_actionPerformed();
- }
- else if (source == findMenuItem)
- {
- findMenuItem_actionPerformed();
- }
- else if (source == font)
- {
- new FontChooser(alignPanel);
- }
- else if (source == newView)
- {
- newView(null);
- }
- else if (source == showColumns)
- {
- viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == showSeqs)
- {
- viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideColumns)
- {
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideSequences
- && viewport.getSelectionGroup() != null)
- {
- viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == hideAllButSelection)
- {
- toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
- }
- else if (source == hideAllSelection)
- {
- SequenceGroup sg = viewport.getSelectionGroup();
- viewport.expandColSelection(sg, false);
- viewport.hideAllSelectedSeqs();
- viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
- }
- else if (source == showAllHidden)
- {
- viewport.showAllHiddenColumns();
- viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
- }
- else if (source == showGroupConsensus)
- {
- showGroupConsensus_actionPerformed();
- }
- else if (source == showGroupConservation)
- {
- showGroupConservation_actionPerformed();
- }
- else if (source == showSequenceLogo)
- {
- showSequenceLogo_actionPerformed();
- }
- else if (source == 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, "Alignment Properties: "
- + getTitle(), 400, 250);
- }
- else if (source == overviewMenuItem)
- {
- overviewMenuItem_actionPerformed();
- }
- else if (source == noColourmenuItem)
- {
- changeColour(null);
- }
- else if (source == clustalColour)
- {
- abovePIDThreshold.setState(false);
- changeColour(new ClustalxColourScheme(viewport.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 == 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 == sortPairwiseMenuItem)
- {
- sortPairwiseMenuItem_actionPerformed();
- }
- else if (source == sortIDMenuItem)
- {
- sortIDMenuItem_actionPerformed();
- }
- else if (source == sortLengthMenuItem)
- {
- sortLengthMenuItem_actionPerformed();
- }
- else if (source == sortGroupMenuItem)
- {
- sortGroupMenuItem_actionPerformed();
- }
- else if (source == removeRedundancyMenuItem)
- {
- removeRedundancyMenuItem_actionPerformed();
- }
- else if (source == pairwiseAlignmentMenuItem)
- {
- pairwiseAlignmentMenuItem_actionPerformed();
- }
- else if (source == PCAMenuItem)
- {
- PCAMenuItem_actionPerformed();
- }
- else if (source == averageDistanceTreeMenuItem)
- {
- averageDistanceTreeMenuItem_actionPerformed();
- }
- else if (source == neighbourTreeMenuItem)
- {
- neighbourTreeMenuItem_actionPerformed();
- }
- else if (source == njTreeBlosumMenuItem)
- {
- njTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == avDistanceTreeBlosumMenuItem)
- {
- avTreeBlosumMenuItem_actionPerformed();
- }
- else if (source == documentation)
- {
- documentation_actionPerformed();
- }
- else if (source == about)
- {
- about_actionPerformed();
- }
-
- }
-
- public void inputText_actionPerformed()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
- }
-
- protected void outputText_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- "Alignment output - " + e.getActionCommand(), 600, 500);
- cap.setText(new AppletFormatAdapter().formatSequences(
- e.getActionCommand(), viewport.getAlignment(),
- viewport.showJVSuffix));
- }
-
- public void loadAnnotations()
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
- cap.setText("Paste your features / annotations / T-coffee score file here.");
- cap.setAnnotationImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
-
- }
-
- public String outputAnnotations(boolean displayTextbox)
- {
- String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).alignmentProperties);
-
- if (displayTextbox)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
- cap.setText(annotation);
- }
-
- return annotation;
- }
-
- private Hashtable getDisplayedFeatureCols()
- {
- if (alignPanel.getFeatureRenderer() != null
- && viewport.featuresDisplayed != null)
- {
- FeatureRenderer fr = alignPanel.getFeatureRenderer();
- Hashtable fcols = new Hashtable();
- Enumeration en = viewport.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- Object col = en.nextElement();
- fcols.put(col, fr.featureColours.get(col));
- }
- return fcols;
- }
- return null;
- }
-
- public String outputFeatures(boolean displayTextbox, String format)
- {
- String features;
- if (format.equalsIgnoreCase("Jalview"))
- {
- features = new FeaturesFile().printJalviewFormat(viewport
- .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, "Features", 600, 500);
- cap.setText(features);
- }
- else
- {
- if (features == null)
- features = "";
- }
-
- return features;
- }
-
- void launchFullApplication()
- {
- StringBuffer url = new StringBuffer(jalviewServletURL);
-
- url.append("?open="
- + appendProtocol(viewport.applet.getParameter("file")));
-
- if (viewport.applet.getParameter("features") != null)
- {
- url.append("&features=");
- url.append(appendProtocol(viewport.applet.getParameter("features")));
- }
-
- if (viewport.applet.getParameter("annotations") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("annotations")));
- }
-
- if (viewport.applet.getParameter("jnetfile") != null)
- {
- url.append("&annotations=");
- url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
- }
-
- if (viewport.applet.getParameter("defaultColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("defaultColour")));
- }
-
- if (viewport.applet.getParameter("userDefinedColour") != null)
- {
- url.append("&colour="
- + removeWhiteSpace(viewport.applet
- .getParameter("userDefinedColour")));
- }
- if (viewport.applet.getParameter("tree") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("tree")));
- }
- if (viewport.applet.getParameter("treeFile") != null)
- {
- url.append("&tree="
- + appendProtocol(viewport.applet.getParameter("treeFile")));
- }
-
- showURL(url.toString(), "FULL_APP");
- }
-
- String removeWhiteSpace(String colour)
- {
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < colour.length(); i++)
- {
- if (Character.isWhitespace(colour.charAt(i)))
- {
- sb.append("%20");
- }
- else
- {
- sb.append(colour.charAt(i));
- }
- }
-
- return sb.toString();
- }
-
- String appendProtocol(String url)
- {
- try
- {
- new URL(url);
- url = URLEncoder.encode(url);
- }
- /*
- * When we finally deprecate 1.1 compatibility, we can start to use
- * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
- * (UnsupportedEncodingException ex) { System.err.println("WARNING -
- * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
- * ex.printStackTrace(); }
- */
- catch (java.net.MalformedURLException ex)
- {
- url = viewport.applet.getCodeBase() + url;
- }
- return url;
- }
-
- public void closeMenuItem_actionPerformed()
- {
- PaintRefresher.RemoveComponent(alignPanel);
- 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.historyList.size() > 0)
- {
- undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
- undoMenuItem.setLabel("Undo " + command.getDescription());
- }
- else
- {
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- }
-
- if (viewport.redoList.size() > 0)
- {
- redoMenuItem.setEnabled(true);
-
- CommandI command = (CommandI) viewport.redoList.peek();
- redoMenuItem.setLabel("Redo " + command.getDescription());
- }
- else
- {
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- }
- }
-
- /**
- * TODO: JAL-1104
- */
- public void addHistoryItem(CommandI command)
- {
- if (command.getSize() > 0)
- {
- viewport.historyList.push(command);
- viewport.redoList.removeAllElements();
- updateEditMenuBar();
- viewport.updateHiddenColumns();
- }
- }
-
- /**
- * TODO: JAL-1104 DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void undoMenuItem_actionPerformed()
- {
- if (viewport.historyList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.historyList.pop();
- viewport.redoList.push(command);
- command.undoCommand(null);
-
- AlignViewport originalSource = getOriginatingSource(command);
- // 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.redoList.size() < 1)
- {
- return;
- }
-
- CommandI command = (CommandI) viewport.redoList.pop();
- viewport.historyList.push(command);
- command.doCommand(null);
-
- AlignViewport 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());
- }
-
- AlignViewport getOriginatingSource(CommandI command)
- {
- AlignViewport originalSource = null;
- // For sequence removal and addition, we need to fire
- // the property change event FROM the viewport where the
- // original alignment was altered
- AlignmentI al = null;
- if (command instanceof EditCommand)
- {
- EditCommand editCommand = (EditCommand) command;
- al = editCommand.getAlignment();
- Vector comps = (Vector) PaintRefresher.components.get(viewport
- .getSequenceSetId());
- for (int i = 0; i < comps.size(); i++)
- {
- if (comps.elementAt(i) instanceof AlignmentPanel)
- {
- if (al == ((AlignmentPanel) comps.elementAt(i)).av.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;
- }
-
- 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);
- }
-
- 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;
- if (viewport.historyList != null && viewport.historyList.size() > 0
- && viewport.historyList.peek() instanceof SlideSequencesCommand)
- {
- appendHistoryItem = ssc
- .appendSlideCommand((SlideSequencesCommand) viewport.historyList
- .peek());
- }
-
- if (!appendHistoryItem)
- addHistoryItem(ssc);
-
- repaint();
- }
-
- static StringBuffer copiedSequences;
-
- static Vector copiedHiddenColumns;
-
- protected void copy_actionPerformed()
- {
- if (viewport.getSelectionGroup() == null)
- {
- return;
- }
-
- SequenceGroup sg = viewport.getSelectionGroup();
- copiedSequences = new StringBuffer();
- Hashtable orderedSeqs = new Hashtable();
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = sg.getSequenceAt(i);
- int index = viewport.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 i = 0; i < viewport.getColumnSelection().getHiddenColumns()
- .size(); i++)
- {
- int[] region = (int[]) viewport.getColumnSelection()
- .getHiddenColumns().elementAt(i);
-
- copiedHiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
- }
- }
- else
- {
- copiedHiddenColumns = null;
- }
-
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI seq = null;
-
- while (seq == null)
- {
- if (orderedSeqs.containsKey(index + ""))
- {
- seq = (SequenceI) orderedSeqs.get(index + "");
- index++;
-
- break;
- }
- else
- {
- index++;
- }
- }
-
- // FIND START RES
- // Returns residue following index if gap
- startRes = seq.findPosition(sg.getStartRes());
-
- // FIND END RES
- // Need to find the residue preceeding index if gap
- endRes = 0;
-
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
- {
- ch = seq.getCharAt(j);
- if (!jalview.util.Comparison.isGap((ch)))
- {
- endRes++;
- }
- }
-
- if (endRes > 0)
- {
- endRes += seq.getStart() - 1;
- }
-
- copiedSequences.append(seq.getName()
- + "\t"
- + startRes
- + "\t"
- + endRes
- + "\t"
- + seq.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1) + "\n");
- }
-
- }
-
- protected void pasteNew_actionPerformed()
- {
- paste(true);
- }
-
- protected void pasteThis_actionPerformed()
- {
- paste(false);
- }
-
- void paste(boolean newAlignment)
- {
- try
- {
-
- if (copiedSequences == null)
- {
- return;
- }
-
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
- Vector seqs = new Vector();
- while (st.hasMoreElements())
- {
- String name = st.nextToken();
- int start = Integer.parseInt(st.nextToken());
- int end = Integer.parseInt(st.nextToken());
- seqs.addElement(new Sequence(name, st.nextToken(), start, end));
- }
- SequenceI[] newSeqs = new SequenceI[seqs.size()];
- for (int i = 0; i < seqs.size(); i++)
- {
- newSeqs[i] = (SequenceI) seqs.elementAt(i);
- }
-
- if (newAlignment)
- {
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
- {
- newtitle = getTitle();
- }
- else
- {
- newtitle = newtitle.concat("- from " + getTitle());
- }
- AlignFrame af = new AlignFrame(new Alignment(newSeqs),
- viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
-
- jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- else
- {
- addSequences(newSeqs);
- }
-
- } catch (Exception ex)
- {
- } // could be anything being pasted in here
-
- }
-
- void addSequences(SequenceI[] seqs)
- {
- for (int i = 0; i < seqs.length; i++)
- {
- viewport.getAlignment().addSequence(seqs[i]);
- }
-
- // !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.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("Cut Sequences", EditCommand.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 (viewport.getSelectionGroup() != null)
- {
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
- // set view properties for each group
- for (int g = 0; g < gps.length; g++)
- {
- // gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
- viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
- viewport.setSequenceColour(sq, col);
- }
- PaintRefresher.Refresh(this, viewport.getSequenceSetId());
- alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
- }
- }
-
- protected void deleteGroups_actionPerformed()
- {
- viewport.getAlignment().deleteAllGroups();
- viewport.sequenceColours = null;
- viewport.setSelectionGroup(null);
-
- alignPanel.paintAlignment(true);
- }
-
- public void selectAllSequenceMenuItem_actionPerformed()
- {
- SequenceGroup sg = new SequenceGroup();
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
- sg.setEndRes(viewport.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("Removed " + trimRegion.getSize() + " columns.");
-
- 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("Removed " + removeGapCols.getSize()
- + " empty columns.");
-
- // 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.historyList = viewport.historyList;
- newaf.viewport.redoList = viewport.redoList;
- return newaf;
- }
-
- /**
- *
- * @return list of feature groups on the view
- */
- public String[] getFeatureGroups()
- {
- FeatureRenderer fr = null;
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- return fr.getGroups();
- }
- return null;
- }
-
- /**
- * get sequence feature groups that are hidden or shown
- *
- * @param visible
- * true is visible
- * @return list
- */
- public String[] getFeatureGroupsOfState(boolean visible)
- {
- FeatureRenderer fr = null;
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- return fr.getGroups(visible);
- }
- return null;
- }
-
- /**
- * Change the display state for the given feature groups
- *
- * @param groups
- * list of group strings
- * @param state
- * visible or invisible
- */
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- FeatureRenderer fr = null;
- this.sequenceFeatures.setState(true);
- viewport.showSequenceFeatures(true);
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
- fr.setGroupState(groups, state);
- alignPanel.seqPanel.seqCanvas.repaint();
- if (alignPanel.overviewPanel != null)
- {
- alignPanel.overviewPanel.updateOverviewImage();
- }
- }
- }
-
- public void seqLimits_itemStateChanged()
- {
- viewport.setShowJVSuffix(seqLimits.getState());
- alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
- }
-
- protected void colourTextMenuItem_actionPerformed()
- {
- viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void displayNonconservedMenuItem_actionPerformed()
- {
- viewport.setShowunconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- protected void wrapMenuItem_actionPerformed()
- {
- viewport.setWrapAlignment(wrapMenuItem.getState());
- alignPanel.setWrapAlignment(wrapMenuItem.getState());
- scaleAbove.setEnabled(wrapMenuItem.getState());
- scaleLeft.setEnabled(wrapMenuItem.getState());
- scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
- }
-
- public void overviewMenuItem_actionPerformed()
- {
- if (alignPanel.overviewPanel != null)
- {
- return;
- }
-
- Frame frame = new Frame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
- frame.add(overview);
- // +50 must allow for applet frame window
- jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
- overview.getPreferredSize().width,
- overview.getPreferredSize().height + 50);
-
- frame.pack();
- final AlignmentPanel ap = alignPanel;
- frame.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent e)
- {
- if (ap != null)
- {
- ap.setOverviewPanel(null);
- }
- };
- });
-
- alignPanel.setOverviewPanel(overview);
-
- }
-
- void changeColour(ColourSchemeI cs)
- {
- int threshold = 0;
-
- if (cs != null)
- {
- if (viewport.getAbovePIDThreshold())
- {
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
-
- cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
- viewport.setGlobalColourScheme(cs);
- }
- else
- {
- cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
- }
-
- if (viewport.getConservationSelected())
- {
-
- Alignment al = (Alignment) viewport.getAlignment();
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
-
- c.calculate();
- c.verdict(false, viewport.getConsPercGaps());
-
- cs.setConservation(c);
-
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
-
- }
- else
- {
- cs.setConservation(null);
- }
-
- cs.setConsensus(viewport.getSequenceConsensusHash());
-
- }
- viewport.setGlobalColourScheme(cs);
-
- if (alignPanel.getOverviewPanel() != null)
- {
- alignPanel.getOverviewPanel().updateOverviewImage();
- }
-
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(viewport.applet)
- .sequenceColoursChanged(alignPanel);
-
- 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, "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("Paste your Newick tree file here.");
- cap.setTreeImport();
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
- }
-
- public void loadTree(jalview.io.NewickFile tree, String treeFile)
- {
- TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
- addTreeMenuItem(tp, treeFile);
- }
-
- /**
- * sort the alignment using the given treePanel
- *
- * @param treePanel
- * tree used to sort view
- * @param title
- * string used for undo event name
- */
- public void sortByTree(TreePanel treePanel, String title)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter
- .sortByTree(viewport.getAlignment(), treePanel.getTree());
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
- // HistoryItem.SORT));
- addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
- viewport.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("JalviewLite - Release " + version, x, y += fh);
- g.setFont(new Font("Helvetica", Font.BOLD, 12));
- g.drawString("Build date: " + builddate, x, y += fh);
- g.setFont(new Font("Helvetica", Font.PLAIN, 12));
- g.drawString(
- "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
- x, y += fh * 1.5);
- g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
- g.drawString(
- "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
- x, y += fh);
- g.drawString(
- "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
- x, y += fh);
- g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
- g.drawString(
- "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
- x, y += fh);
- g.drawString(
- "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
- x, y += fh);
- g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
- x, y += fh);
- }
- }
-
- Frame frame = new Frame();
- frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
- .getBuildDate()));
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
-
- }
-
- public void showURL(String url, String target)
- {
- if (viewport.applet == null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- viewport.applet.showURL(url, target);
- }
- }
-
- // ////////////////////////////////////////////////////////////////////////////////
- // JBuilder Graphics here
-
- MenuBar alignFrameMenuBar = new MenuBar();
-
- Menu fileMenu = new Menu("File");
-
- MenuItem loadApplication = new MenuItem("View in Full Application");
-
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");
-
- MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-
- MenuItem outputFeatures = new MenuItem("Export Features ...");
-
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
-
- MenuItem closeMenuItem = new MenuItem("Close");
-
- Menu editMenu = new Menu("Edit");
-
- Menu viewMenu = new Menu("View");
-
- Menu colourMenu = new Menu("Colour");
-
- Menu calculateMenu = new Menu("Calculate");
-
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
-
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
-
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
-
- MenuItem remove2LeftMenuItem = new MenuItem();
-
- MenuItem remove2RightMenuItem = new MenuItem();
-
- MenuItem removeGappedColumnMenuItem = new MenuItem();
-
- MenuItem removeAllGapsMenuItem = new MenuItem();
-
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
-
- MenuItem sortPairwiseMenuItem = new MenuItem();
-
- MenuItem sortIDMenuItem = new MenuItem();
-
- MenuItem sortLengthMenuItem = new MenuItem();
-
- MenuItem sortGroupMenuItem = new MenuItem();
-
- MenuItem removeRedundancyMenuItem = new MenuItem();
-
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();
-
- MenuItem PCAMenuItem = new MenuItem();
-
- MenuItem averageDistanceTreeMenuItem = new MenuItem();
-
- MenuItem neighbourTreeMenuItem = new MenuItem();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- public Label statusBar = new Label();
-
- Menu outputTextboxMenu = new Menu();
-
- MenuItem clustalColour = new MenuItem();
-
- MenuItem zappoColour = new MenuItem();
-
- MenuItem taylorColour = new MenuItem();
-
- MenuItem hydrophobicityColour = new MenuItem();
-
- MenuItem helixColour = new MenuItem();
-
- MenuItem strandColour = new MenuItem();
-
- MenuItem turnColour = new MenuItem();
-
- MenuItem buriedColour = new MenuItem();
-
- MenuItem purinePyrimidineColour = 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("Alignment Properties...");
-
- MenuItem overviewMenuItem = new MenuItem();
-
- MenuItem undoMenuItem = new MenuItem();
-
- MenuItem redoMenuItem = new MenuItem();
-
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
-
- MenuItem noColourmenuItem = new MenuItem();
-
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
-
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
-
- MenuItem findMenuItem = new MenuItem();
-
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
-
- MenuItem nucleotideColour = new MenuItem();
-
- MenuItem deleteGroups = new MenuItem();
-
- MenuItem grpsFromSelection = new MenuItem();
-
- MenuItem delete = new MenuItem();
-
- MenuItem copy = new MenuItem();
-
- MenuItem cut = new MenuItem();
-
- Menu pasteMenu = new Menu();
-
- MenuItem pasteNew = new MenuItem();
-
- MenuItem pasteThis = new MenuItem();
-
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
-
- MenuItem font = new MenuItem();
-
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
-
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
-
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();
-
- MenuItem modifyPID = new MenuItem();
-
- MenuItem modifyConservation = new MenuItem();
-
- CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
- "Autocalculate Consensus", true);
-
- CheckboxMenuItem sortByTree = new CheckboxMenuItem(
- "Sort Alignment With New Tree", true);
-
- Menu sortByTreeMenu = new Menu();
-
- Menu sort = new Menu();
-
- Menu calculate = new Menu();
-
- MenuItem inputText = new MenuItem();
-
- Menu helpMenu = new Menu();
-
- MenuItem documentation = new MenuItem();
-
- MenuItem about = new MenuItem();
-
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();
-
- CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
-
- CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
-
- Menu autoAnnMenu = new Menu();
-
- CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
-
- CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
-
- CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
-
- CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
-
- CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
-
- CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
-
- private void jbInit() throws Exception
- {
-
- setMenuBar(alignFrameMenuBar);
-
- MenuItem item;
-
- // dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
-
- item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @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);
- selectAllSequenceMenuItem.addActionListener(this);
- deselectAllSequenceMenuItem.addActionListener(this);
- invertSequenceMenuItem.addActionListener(this);
- remove2LeftMenuItem.setLabel("Remove Left");
- remove2LeftMenuItem.addActionListener(this);
- remove2RightMenuItem.setLabel("Remove Right");
- remove2RightMenuItem.addActionListener(this);
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
- removeGappedColumnMenuItem.addActionListener(this);
- removeAllGapsMenuItem.setLabel("Remove All Gaps");
- removeAllGapsMenuItem.addActionListener(this);
- viewBoxesMenuItem.setLabel("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addItemListener(this);
- viewTextMenuItem.setLabel("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.addItemListener(this);
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(this);
- sortIDMenuItem.setLabel("by ID");
- sortIDMenuItem.addActionListener(this);
- sortLengthMenuItem.setLabel("by Length");
- sortLengthMenuItem.addActionListener(this);
- sortGroupMenuItem.setLabel("by Group");
- sortGroupMenuItem.addActionListener(this);
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");
- removeRedundancyMenuItem.addActionListener(this);
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.addActionListener(this);
- PCAMenuItem.setLabel("Principal Component Analysis");
- PCAMenuItem.addActionListener(this);
- averageDistanceTreeMenuItem
- .setLabel("Average Distance Using % Identity");
- averageDistanceTreeMenuItem.addActionListener(this);
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(this);
- statusBar.setBackground(Color.white);
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
- statusBar.setText("Status bar");
- outputTextboxMenu.setLabel("Output to Textbox");
- clustalColour.setLabel("Clustalx");
-
- clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
- zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix Propensity");
- helixColour.addActionListener(this);
- strandColour.setLabel("Strand Propensity");
- strandColour.addActionListener(this);
- turnColour.setLabel("Turn Propensity");
- turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
- buriedColour.addActionListener(this);
- purinePyrimidineColour.setLabel("Purine/Pyrimidine");
- purinePyrimidineColour.addActionListener(this);
- RNAHelixColour.setLabel("by RNA Helices");
- RNAHelixColour.addActionListener(this);
- userDefinedColour.setLabel("User Defined...");
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62 Score");
- BLOSUM62Colour.addActionListener(this);
- tcoffeeColour.setLabel("T-Coffee Scores");
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
- // provided
- tcoffeeColour.addActionListener(this);
- avDistanceTreeBlosumMenuItem
- .setLabel("Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(this);
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(this);
- annotationPanelMenuItem.setLabel("Show Annotations");
- annotationPanelMenuItem.addItemListener(this);
- colourTextMenuItem.setLabel("Colour Text");
- colourTextMenuItem.addItemListener(this);
- displayNonconservedMenuItem.setLabel("Show nonconserved");
- displayNonconservedMenuItem.addItemListener(this);
- alProperties.addActionListener(this);
- overviewMenuItem.setLabel("Overview Window");
- overviewMenuItem.addActionListener(this);
- undoMenuItem.setEnabled(false);
- undoMenuItem.setLabel("Undo");
- undoMenuItem.addActionListener(this);
- redoMenuItem.setEnabled(false);
- redoMenuItem.setLabel("Redo");
- redoMenuItem.addActionListener(this);
- conservationMenuItem.setLabel("by Conservation");
- conservationMenuItem.addItemListener(this);
- noColourmenuItem.setLabel("None");
- noColourmenuItem.addActionListener(this);
- wrapMenuItem.setLabel("Wrap");
- wrapMenuItem.addItemListener(this);
- renderGapsMenuItem.setLabel("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addItemListener(this);
- findMenuItem.setLabel("Find...");
- findMenuItem.addActionListener(this);
- abovePIDThreshold.setLabel("Above Identity Threshold");
- abovePIDThreshold.addItemListener(this);
- nucleotideColour.setLabel("Nucleotide");
- nucleotideColour.addActionListener(this);
- deleteGroups.setLabel("Undefine Groups");
- deleteGroups.addActionListener(this);
- grpsFromSelection.setLabel("Make Groups for selection");
- grpsFromSelection.addActionListener(this);
- copy.setLabel("Copy");
- copy.addActionListener(this);
- cut.setLabel("Cut");
- cut.addActionListener(this);
- delete.setLabel("Delete");
- delete.addActionListener(this);
- pasteMenu.setLabel("Paste");
- pasteNew.setLabel("To New Alignment");
- pasteNew.addActionListener(this);
- pasteThis.setLabel("Add To This Alignment");
- pasteThis.addActionListener(this);
- applyToAllGroups.setLabel("Apply Colour To All Groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addItemListener(this);
- font.setLabel("Font...");
- font.addActionListener(this);
- scaleAbove.setLabel("Scale Above");
- scaleAbove.setState(true);
- scaleAbove.setEnabled(false);
- scaleAbove.addItemListener(this);
- scaleLeft.setEnabled(false);
- scaleLeft.setState(true);
- scaleLeft.setLabel("Scale Left");
- scaleLeft.addItemListener(this);
- scaleRight.setEnabled(false);
- scaleRight.setState(true);
- scaleRight.setLabel("Scale Right");
- scaleRight.addItemListener(this);
- modifyPID.setLabel("Modify Identity Threshold...");
- modifyPID.addActionListener(this);
- modifyConservation.setLabel("Modify Conservation Threshold...");
- modifyConservation.addActionListener(this);
- sortByTreeMenu.setLabel("By Tree Order");
- sort.setLabel("Sort");
- calculate.setLabel("Calculate Tree");
- autoCalculate.addItemListener(this);
- sortByTree.addItemListener(this);
- inputText.setLabel("Input from textbox");
- inputText.addActionListener(this);
- centreColumnLabelFlag.setLabel("Centre column labels");
- centreColumnLabelFlag.addItemListener(this);
- followMouseOverFlag.setLabel("Automatic Scrolling");
- followMouseOverFlag.addItemListener(this);
- helpMenu.setLabel("Help");
- documentation.setLabel("Documentation");
- documentation.addActionListener(this);
-
- about.setLabel("About...");
- about.addActionListener(this);
- seqLimits.setState(true);
- seqLimits.setLabel("Show Sequence Limits");
- seqLimits.addItemListener(this);
- featureSettings.setLabel("Feature Settings...");
- featureSettings.addActionListener(this);
- sequenceFeatures.setLabel("Sequence Features");
- sequenceFeatures.addItemListener(this);
- sequenceFeatures.setState(false);
- annotationColour.setLabel("by Annotation...");
- annotationColour.addActionListener(this);
- invertSequenceMenuItem.setLabel("Invert Sequence Selection");
- invertColSel.setLabel("Invert Column Selection");
- menu1.setLabel("Show");
- showColumns.setLabel("All Columns ");
- showSeqs.setLabel("All Sequences");
- menu2.setLabel("Hide");
- hideColumns.setLabel("Selected Columns");
- hideSequences.setLabel("Selected Sequences");
- hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
- hideAllSelection.setLabel("Selected Region");
- showAllHidden.setLabel("All Sequences and Columns");
- showGroupConsensus.setLabel("Group Consensus");
- showGroupConservation.setLabel("Group Conservation");
- showConsensusHistogram.setLabel("Show Consensus Histogram");
- showSequenceLogo.setLabel("Show Consensus Logo");
- normSequenceLogo.setLabel("Normalise Consensus Logo");
- applyAutoAnnotationSettings.setLabel("Apply to all groups");
- applyAutoAnnotationSettings.setState(true);
- autoAnnMenu.setLabel("Autocalculated Annotation");
-
- invertColSel.addActionListener(this);
- showColumns.addActionListener(this);
- showSeqs.addActionListener(this);
- hideColumns.addActionListener(this);
- hideSequences.addActionListener(this);
- hideAllButSelection.addActionListener(this);
- hideAllSelection.addActionListener(this);
- showAllHidden.addActionListener(this);
- showGroupConsensus.addItemListener(this);
- showGroupConservation.addItemListener(this);
- showConsensusHistogram.addItemListener(this);
- showSequenceLogo.addItemListener(this);
- normSequenceLogo.addItemListener(this);
-
- applyAutoAnnotationSettings.addItemListener(this);
- formatMenu.setLabel("Format");
- selectMenu.setLabel("Select");
- newView.setLabel("New View");
- newView.addActionListener(this);
- alignFrameMenuBar.add(fileMenu);
- alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(selectMenu);
- alignFrameMenuBar.add(viewMenu);
- alignFrameMenuBar.add(formatMenu);
- alignFrameMenuBar.add(colourMenu);
- alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(helpMenu);
-
- fileMenu.add(inputText);
- fileMenu.add(loadTree);
- fileMenu.add(loadAnnotations);
-
- fileMenu.addSeparator();
- fileMenu.add(outputTextboxMenu);
- fileMenu.add(outputFeatures);
- fileMenu.add(outputAnnotations);
-
- if (jalviewServletURL != null)
- {
- fileMenu.add(loadApplication);
- }
-
- fileMenu.addSeparator();
- fileMenu.add(closeMenuItem);
-
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.add(cut);
- editMenu.add(copy);
- editMenu.add(pasteMenu);
- editMenu.add(delete);
- editMenu.addSeparator();
- editMenu.add(remove2LeftMenuItem);
- editMenu.add(remove2RightMenuItem);
- editMenu.add(removeGappedColumnMenuItem);
- editMenu.add(removeAllGapsMenuItem);
- editMenu.add(removeRedundancyMenuItem);
- viewMenu.add(newView);
- viewMenu.addSeparator();
- viewMenu.add(menu1);
- viewMenu.add(menu2);
- viewMenu.addSeparator();
- viewMenu.add(followMouseOverFlag);
- viewMenu.add(annotationPanelMenuItem);
- autoAnnMenu.add(applyAutoAnnotationSettings);
- autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showSequenceLogo);
- autoAnnMenu.add(normSequenceLogo);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- viewMenu.add(autoAnnMenu);
- viewMenu.addSeparator();
- viewMenu.add(sequenceFeatures);
- viewMenu.add(featureSettings);
- viewMenu.addSeparator();
- viewMenu.add(alProperties);
- viewMenu.addSeparator();
- viewMenu.add(overviewMenuItem);
- colourMenu.add(applyToAllGroups);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- 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);
- calculateMenu.add(sort);
- calculateMenu.add(calculate);
- calculateMenu.addSeparator();
- calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
- calculateMenu.add(autoCalculate);
- calculateMenu.add(sortByTree);
- this.add(statusBar, BorderLayout.SOUTH);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortByTreeMenu);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- helpMenu.add(documentation);
- helpMenu.add(about);
- menu1.add(showColumns);
- menu1.add(showSeqs);
- menu1.add(showAllHidden);
- menu2.add(hideColumns);
- menu2.add(hideSequences);
- menu2.add(hideAllSelection);
- menu2.add(hideAllButSelection);
- formatMenu.add(font);
- formatMenu.add(seqLimits);
- formatMenu.add(wrapMenuItem);
- formatMenu.add(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(viewBoxesMenuItem);
- formatMenu.add(viewTextMenuItem);
- formatMenu.add(colourTextMenuItem);
- formatMenu.add(displayNonconservedMenuItem);
- formatMenu.add(renderGapsMenuItem);
- formatMenu.add(centreColumnLabelFlag);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- selectMenu.add(deselectAllSequenceMenuItem);
- selectMenu.add(invertSequenceMenuItem);
- selectMenu.add(invertColSel);
- selectMenu.add(grpsFromSelection);
- selectMenu.add(deleteGroups);
-
- }
-
- MenuItem featureSettings = new MenuItem();
-
- CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
-
- MenuItem annotationColour = new MenuItem();
-
- MenuItem invertColSel = new MenuItem();
-
- Menu menu1 = new Menu();
-
- MenuItem showColumns = new MenuItem();
-
- MenuItem showSeqs = new MenuItem();
-
- Menu menu2 = new Menu();
-
- MenuItem hideColumns = new MenuItem();
-
- MenuItem hideSequences = new MenuItem();
-
- MenuItem hideAllButSelection = new MenuItem();
-
- MenuItem hideAllSelection = new MenuItem();
-
- MenuItem showAllHidden = new MenuItem();
-
- Menu formatMenu = new Menu();
-
- Menu selectMenu = new Menu();
-
- MenuItem newView = new MenuItem();
-
- /**
- * Attach the alignFrame panels after embedding menus, if necessary. This used
- * to be called setEmbedded, but is now creates the dropdown menus in a
- * platform independent manner to avoid OSX/Mac menu appendage daftness.
- *
- * @param reallyEmbedded
- * true to attach the view to the applet area on the page rather than
- * in a new window
- */
- public void createAlignFrameWindow(boolean reallyEmbedded, String title)
- {
- if (reallyEmbedded)
- {
- // ////
- // Explicly build the embedded menu panel for the on-page applet
- //
- // view cannot be closed if its actually on the page
- fileMenu.remove(closeMenuItem);
- fileMenu.remove(3); // Remove Seperator
- embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
- Font.PLAIN, 10, false); // use our own fonts.
- // and actually add the components to the applet area
- viewport.applet.setLayout(new BorderLayout());
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
- viewport.applet.add(statusBar, BorderLayout.SOUTH);
- alignPanel.setSize(viewport.applet.getSize().width,
- viewport.applet.getSize().height - embeddedMenu.HEIGHT
- - statusBar.HEIGHT);
- viewport.applet.add(alignPanel, BorderLayout.CENTER);
- final AlignFrame me = this;
- viewport.applet.addFocusListener(new FocusListener()
- {
-
- @Override
- public void focusLost(FocusEvent e)
- {
- if (me.viewport.applet.currentAlignFrame == me)
- {
- me.viewport.applet.currentAlignFrame = null;
- }
- }
-
- @Override
- public void focusGained(FocusEvent e)
- {
- me.viewport.applet.currentAlignFrame = me;
- }
- });
- viewport.applet.validate();
- }
- else
- {
- // //////
- // test and embed menu bar if necessary.
- //
- if (embedMenuIfNeeded(alignPanel))
- {
- // adjust for status bar height too
- alignPanel.setSize(getSize().width, getSize().height
- - statusBar.HEIGHT);
- }
- add(statusBar, BorderLayout.SOUTH);
- add(alignPanel, BorderLayout.CENTER);
- // and register with the applet so it can pass external API calls to us
- jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- }
- }
-
- /**
- * create a new binding between structures in an existing jmol viewer instance
- * and an alignpanel with sequences that have existing PDBFile entries. Note,
- * this does not open a new Jmol window, or modify the display of the
- * structures in the original jmol window. Note This method doesn't work
- * without an additional javascript library to exchange messages between the
- * distinct applets. See http://issues.jalview.org/browse/JAL-621
- *
- * @param viewer
- * JmolViewer instance
- * @param sequenceIds
- * - sequence Ids to search for associations
- */
- public SequenceStructureBinding addStructureViewInstance(
- Object jmolviewer, String[] sequenceIds)
- {
- org.jmol.api.JmolViewer viewer = null;
- try
- {
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
- } catch (ClassCastException ex)
- {
- System.err.println("Unsupported viewer object :"
- + jmolviewer.getClass());
- }
- if (viewer == null)
- {
- System.err.println("Can't use this object as a structure viewer:"
- + jmolviewer.getClass());
- return null;
- }
- SequenceI[] seqs = null;
- if (sequenceIds == null || sequenceIds.length == 0)
- {
- seqs = viewport.getAlignment().getSequencesArray();
- }
- else
- {
- Vector sqi = new Vector();
- AlignmentI al = viewport.getAlignment();
- for (int sid = 0; sid < sequenceIds.length; sid++)
- {
- SequenceI sq = al.findName(sequenceIds[sid]);
- if (sq != null)
- {
- sqi.addElement(sq);
- }
- }
- if (sqi.size() > 0)
- {
- seqs = new SequenceI[sqi.size()];
- for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
- {
- seqs[sid] = (SequenceI) sqi.elementAt(sid);
- }
- }
- else
- {
- return null;
- }
- }
- ExtJmol jmv = null;
- // TODO: search for a jmv that involves viewer
- if (jmv == null)
- { // create a new viewer/jalview binding.
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
- { seqs });
- }
- return jmv;
-
- }
-
- /**
- * bind a pdb file to a sequence in the current view
- *
- * @param sequenceId
- * - sequenceId within the dataset.
- * @param pdbEntryString
- * - the short name for the PDB file
- * @param pdbFile
- * - pdb file - either a URL or a valid PDB file.
- * @return true if binding was as success TODO: consider making an exception
- * structure for indicating when PDB parsing or sequenceId location
- * fails.
- */
- public boolean addPdbFile(String sequenceId, String pdbEntryString,
- String pdbFile)
- {
- SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
- boolean needtoadd = false;
- if (toaddpdb != null)
- {
- Vector pdbe = toaddpdb.getPDBId();
- PDBEntry pdbentry = null;
- if (pdbe != null && pdbe.size() > 0)
- {
- for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
- {
- pdbentry = (PDBEntry) pdbe.elementAt(pe);
- if (!pdbentry.getId().equals(pdbEntryString)
- && !pdbentry.getFile().equals(pdbFile))
- {
- pdbentry = null;
- }
- else
- {
- continue;
- }
- }
- }
- if (pdbentry == null)
- {
- pdbentry = new PDBEntry();
- pdbentry.setId(pdbEntryString);
- pdbentry.setFile(pdbFile);
- needtoadd = true; // add this new entry to sequence.
- }
- // resolve data source
- // TODO: this code should be a refactored to an io package
- String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
- if (protocol == null)
- {
- return false;
- }
- if (needtoadd)
- {
- // make a note of the access mode and add
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- }
- pdbentry.getProperty().put("protocol", protocol);
- toaddpdb.addPDBId(pdbentry);
- }
- }
- return true;
- }
-
- private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
- {
- if (seqs != null)
- {
- Vector sequences = new Vector();
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- sequences.addElement(new Object[]
- { seqs[i], (chains != null) ? chains[i] : null });
- }
- }
- seqs = new SequenceI[sequences.size()];
- chains = new String[sequences.size()];
- for (int i = 0, isize = sequences.size(); i < isize; i++)
- {
- Object[] oj = (Object[]) sequences.elementAt(i);
-
- seqs[i] = (SequenceI) oj[0];
- chains[i] = (String) oj[1];
- }
- }
- return new Object[]
- { seqs, chains };
-
- }
-
- public void newStructureView(JalviewLite applet, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, String protocol)
- {
- // Scrub any null sequences from the array
- Object[] sqch = cleanSeqChainArrays(seqs, chains);
- seqs = (SequenceI[]) sqch[0];
- chains = (String[]) sqch[1];
- if (seqs == null || seqs.length == 0)
- {
- System.err
- .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
- }
- if (protocol == null || protocol.trim().length() == 0
- || protocol.equals("null"))
- {
- protocol = (String) pdb.getProperty().get("protocol");
- if (protocol == null)
- {
- System.err.println("Couldn't work out protocol to open structure: "
- + pdb.getId());
- return;
- }
- }
- if (applet.useXtrnalSviewer)
- {
- // register the association(s) and quit, don't create any windows.
- if (StructureSelectionManager.getStructureSelectionManager(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;
- }
-
-}
+/*\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
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
++ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
++ * \r
+ * This file is part of Jalview.\r
- *\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
++ * 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
++ * \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
++ * \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.RNAInteractionColourScheme;\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
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+\r
- public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
++public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
++ 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
++ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
++ 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
++ else\r
++ {\r
+ RNAHelixColour.setEnabled(false);\r
+ }\r
- } else {\r
++ }\r
++ else\r
++ {\r
+ RNAHelixColour.setEnabled(false);\r
+ purinePyrimidineColour.setEnabled(false);\r
+ }\r
- \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
++ * @param file\r
++ * file URL, content, or other resolvable path\r
++ * @param type\r
++ * 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
++ * \r
++ * @param file\r
++ * file URL, content, or other resolvable path\r
++ * @param type\r
++ * is protocol for accessing data referred to by file\r
++ * @param autoenabledisplay\r
++ * when true, display features flag will be automatically enabled if\r
++ * 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
++ public boolean parseFeaturesFile(String file, String type,\r
++ 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
++ // TODO: test if importing a features file onto an alignment which already\r
++ // 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
++ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas\r
++ .getFeatureRenderer().featureColours, featureLinks,\r
++ true, viewport.applet.getDefaultParameter(\r
++ "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
++ * \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
++ if ((viewport.getColumnSelection() != null\r
++ && viewport.getColumnSelection().getSelected() != null && viewport\r
++ .getColumnSelection().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
++ else if (!(toggleCols && viewport.getColumnSelection().getSelected()\r
++ .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
++ 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 == RNAInteractionColour)\r
+ {\r
+ changeColour(new RNAInteractionColourScheme());\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
++ else if (source == tcoffeeColour)\r
++ {\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
++ .getAlignmentAnnotation() : null, viewport\r
++ .getAlignment().getGroups(), ((Alignment) viewport\r
++ .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
++ if (alignPanel.getFeatureRenderer() != null\r
++ && 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
++ features = new FeaturesFile().printJalviewFormat(viewport\r
++ .getAlignment().getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
+ }\r
+ else\r
+ {\r
- features = new FeaturesFile().printGFFFormat(\r
- viewport.getAlignment().getSequencesArray(),\r
- getDisplayedFeatureCols());\r
++ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()\r
++ .getSequencesArray(), getDisplayedFeatureCols());\r
+ }\r
+\r
+ if (displayTextbox)\r
+ {\r
- boolean frimport=false;\r
- if (features==null || features.equals("No Features Visible"))\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
++ 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
++ }\r
++ else\r
++ {\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
++ if (alignPanel.seqPanel != null\r
++ && alignPanel.seqPanel.seqCanvas != null)\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ }\r
- if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {\r
++ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)\r
++ {\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
++ else\r
++ {\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
++ * TODO: JAL-1104 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
++ if (originalSource != viewport)\r
++ {\r
++ System.err\r
++ .println("Warning: Viewport object mismatch whilst undoing");\r
+ }\r
- originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;\r
++ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =\r
++ // viewport.getColumnSelection().getHiddenColumns()\r
++ // != null;\r
+ updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
++ originalSource.firePropertyChange("alignment", null, originalSource\r
++ .getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
- * TODO: JAL-1104\r
- * DOCUMENT ME!\r
- *\r
++ * TODO: JAL-1104 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
++ if (originalSource != viewport)\r
++ {\r
++ System.err\r
++ .println("Warning: Viewport object mismatch whilst re-doing");\r
+ }\r
- originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;\r
++ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =\r
++ // viewport.getColumnSelection().getHiddenColumns()\r
++ // != null;\r
+\r
+ updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
++ originalSource.firePropertyChange("alignment", null, originalSource\r
++ .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
++ viewport.getAlignment().moveSelectedSequencesByOne(sg,\r
++ 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
++ List<SequenceI> sg = new Vector<SequenceI>();\r
+ if (viewport.cursorMode)\r
+ {\r
- sg.add(viewport.getAlignment()\r
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
++ sg.add(viewport.getAlignment().getSequenceAt(\r
++ alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() != viewport.getAlignment()\r
- .getHeight())\r
++ && viewport.getSelectionGroup().getSize() != viewport\r
++ .getAlignment().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
++ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup\r
++ .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
++ seqs, 0, viewport.getAlignment().getWidth(),\r
++ viewport.getAlignment()));\r
+\r
+ viewport.setEndSeq(viewport.getAlignment().getHeight());\r
+ viewport.getAlignment().getWidth();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
++ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
++ .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
+ */\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
++ * \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
+ /*\r
+ * (non-Javadoc)\r
- *\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
+\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.getGapCharacter()), viewport.getAlignment()\r
++ .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
++ viewport.setSequenceColour(sq, col);\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
++ 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
++ "Remove Gapped Columns", seqs, start, end,\r
++ 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
++ * \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
++ newal.addAnnotation(viewport.getAlignment()\r
++ .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
++ * \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
++ * \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
++ * \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
++ final AlignmentPanel ap = alignPanel;\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ @Override\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
- if (ap!=null) {\r
++ if (ap != null)\r
++ {\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
++ .getStructureSelectionManager(viewport.applet)\r
++ .sequenceColoursChanged(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
++ addHistoryItem(new OrderCommand("ID Sort", oldOrder,\r
++ 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.getSelectionGroup() == null && viewport.getAlignment()\r
- .getHeight() > 1))\r
++ || (viewport.getAlignment().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
++ * \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
++ * \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
++\r
+ public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+ {\r
- SequenceI[] oldOrder = viewport.getAlignment()\r
- .getSequencesArray();\r
++ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ if (viewport.applet.debug)\r
+ {\r
- System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
++ System.err.println("Sorting " + alorder.getOrder().size()\r
++ + " in alignment '" + getTitle() + "'");\r
+ }\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
- if (undoname!=null)\r
++ if (undoname != null)\r
+ {\r
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));\r
++ addHistoryItem(new OrderCommand(undoname, oldOrder,\r
++ 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
++ "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",\r
+ x, y += fh * 1.5);\r
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
++ g.drawString(\r
++ "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",\r
++ x + 50, y += fh + 8);\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
++\r
+ MenuItem RNAInteractionColour = new MenuItem();\r
++\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
++\r
++ Menu autoAnnMenu = new Menu();\r
++\r
++ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();\r
++\r
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
++\r
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
++\r
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
++\r
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\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
+ RNAInteractionColour.setLabel("Purine/Pyrimidine");\r
+ RNAInteractionColour.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.setEnabled(false); // it will enabled only if a score file is\r
++ // provided\r
+ tcoffeeColour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");\r
++ avDistanceTreeBlosumMenuItem\r
++ .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
+ 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(RNAInteractionColour);\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
++ * \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
++ if (me.viewport.applet.currentAlignFrame == me)\r
++ {\r
++ me.viewport.applet.currentAlignFrame = null;\r
++ }\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
++ * \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
++ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]\r
++ { seqs });\r
+ }\r
+ return jmv;\r
+\r
+ }\r
++\r
+ /**\r
+ * bind a pdb file to a sequence in the current view\r
- *\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
++ if (StructureSelectionManager.getStructureSelectionManager(applet)\r
++ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)\r
++ {\r
++ System.err.println("Failed to map " + pdb.getFile() + " ("\r
++ + 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
++ * modify the current selection, providing the user has not made a selection\r
++ * already.\r
++ * \r
++ * @param sel\r
++ * - sequences from this alignment\r
++ * @param csel\r
++ * - 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
++\r
+ public void scrollToRow(int row)\r
+ {\r
+ alignPanel.seqPanel.scrollToRow(row);\r
+ }\r
++\r
+ public void scrollToColumn(int column)\r
+ {\r
+ alignPanel.seqPanel.scrollToColumn(column);\r
+ }\r
++\r
+ /**\r
+ * @return the alignments unique ID.\r
+ */\r
- public String getSequenceSetId() {\r
++ public String getSequenceSetId()\r
++ {\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
++ * \r
++ * @param source\r
++ * File/URL/T-COFFEE score file contents\r
+ * @throws IOException\r
+ * @return true if alignment was annotated with data from source\r
- * @throws SAXException \r
- * @throws ParserConfigurationException \r
- * @throws ExceptionFileFormatOrSyntax \r
- * @throws ExceptionLoadingFailed \r
- * @throws ExceptionPermissionDenied \r
- * @throws InterruptedException \r
- * @throws ExceptionUnmatchedClosingParentheses \r
++ * @throws SAXException\r
++ * @throws ParserConfigurationException\r
++ * @throws ExceptionFileFormatOrSyntax\r
++ * @throws ExceptionLoadingFailed\r
++ * @throws ExceptionPermissionDenied\r
++ * @throws InterruptedException\r
++ * @throws ExceptionUnmatchedClosingParentheses\r
+ */\r
- public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {\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
++ public boolean loadScoreFile(String source) throws IOException,\r
++ ExceptionFileFormatOrSyntax, ParserConfigurationException,\r
++ SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,\r
++ InterruptedException, ExceptionUnmatchedClosingParentheses\r
++ {\r
++\r
++ TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r
++ AppletFormatAdapter.checkProtocol(source));\r
++ if (!file.isValid())\r
++ {\r
++ // TODO: raise dialog for gui\r
++ System.err.println("Problems parsing T-Coffee scores: "\r
++ + 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\r
++ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file\r
++ .getWidth()))\r
++ {\r
++ // TODO: raise a dialog box here rather than bomb out.\r
++ System.err\r
++ .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
++ }\r
++ else\r
++ {\r
++ System.err.println("Problems resolving T-Coffee scores:");\r
++ if (file.getWarningMessage() != null)\r
++ {\r
++ System.err.println(file.getWarningMessage());\r
++ }\r
++ }\r
++ return false;\r
++ }\r
+\r
+}\r
- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\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
+ /*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.Format;
-
-/**
- * Parse and create Jalview Features files Detects GFF format features files and
- * parses. Does not implement standard print() - call specific printFeatures or
- * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
- * for the features annotation - this normally works on an exact match.
- *
- * @author AMW
- * @version $Revision$
- */
-public class FeaturesFile extends AlignFile
-{
- /**
- * work around for GFF interpretation bug where source string becomes
- * description rather than a group
- */
- private boolean doGffSource = true;
-
- /**
- * Creates a new FeaturesFile object.
- */
- public FeaturesFile()
- {
- }
-
- /**
- * Creates a new FeaturesFile object.
- *
- * @param inFile
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public FeaturesFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public FeaturesFile(FileParse source) throws IOException
- {
- super(source);
- }
-
- /**
- * Parse GFF or sequence features file using case-independent matching,
- * discarding URLs
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param removeHTML
- * - process html strings into plain text
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Hashtable colours,
- boolean removeHTML)
- {
- return parse(align, colours, null, removeHTML, false);
- }
-
- /**
- * Parse GFF or sequence features file optionally using case-independent
- * matching, discarding URLs
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param removeHTML
- * - process html strings into plain text
- * @param relaxedIdmatching
- * - when true, ID matches to compound sequence IDs are allowed
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Map colours, boolean removeHTML,
- boolean relaxedIdMatching)
- {
- return parse(align, colours, null, removeHTML, relaxedIdMatching);
- }
-
- /**
- * Parse GFF or sequence features file optionally using case-independent
- * matching
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param featureLink
- * - hashtable to store associated URLs
- * @param removeHTML
- * - process html strings into plain text
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML)
- {
- return parse(align, colours, featureLink, removeHTML, false);
- }
-
- /**
- * /** Parse GFF or sequence features file
- *
- * @param align
- * - alignment/dataset containing sequences that are to be annotated
- * @param colours
- * - hashtable to store feature colour definitions
- * @param featureLink
- * - hashtable to store associated URLs
- * @param removeHTML
- * - process html strings into plain text
- * @param relaxedIdmatching
- * - when true, ID matches to compound sequence IDs are allowed
- * @return true if features were added
- */
- public boolean parse(AlignmentI align, Map colours, Map featureLink,
- boolean removeHTML, boolean relaxedIdmatching)
- {
-
- String line = null;
- try
- {
- SequenceI seq = null;
- String type, desc, token = null;
-
- int index, start, end;
- float score;
- StringTokenizer st;
- SequenceFeature sf;
- String featureGroup = null, groupLink = null;
- Map typeLink = new Hashtable();
- /**
- * when true, assume GFF style features rather than Jalview style.
- */
- boolean GFFFile = true;
- while ((line = nextLine()) != null)
- {
- if (line.startsWith("#"))
- {
- continue;
- }
-
- st = new StringTokenizer(line, "\t");
- if (st.countTokens() == 1)
- {
- if (line.trim().equalsIgnoreCase("GFF"))
- {
- // Start parsing file as if it might be GFF again.
- GFFFile = true;
- continue;
- }
- }
- if (st.countTokens() > 1 && st.countTokens() < 4)
- {
- GFFFile = false;
- type = st.nextToken();
- if (type.equalsIgnoreCase("startgroup"))
- {
- featureGroup = st.nextToken();
- if (st.hasMoreElements())
- {
- groupLink = st.nextToken();
- featureLink.put(featureGroup, groupLink);
- }
- }
- else if (type.equalsIgnoreCase("endgroup"))
- {
- // We should check whether this is the current group,
- // but at present theres no way of showing more than 1 group
- st.nextToken();
- featureGroup = null;
- groupLink = null;
- }
- else
- {
- Object colour = null;
- String colscheme = st.nextToken();
- if (colscheme.indexOf("|") > -1
- || colscheme.trim().equalsIgnoreCase("label"))
- {
- // Parse '|' separated graduated colourscheme fields:
- // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
- // can either provide 'label' only, first is optional, next two
- // colors are required (but may be
- // left blank), next is optional, nxt two min/max are required.
- // first is either 'label'
- // first/second and third are both hexadecimal or word equivalent
- // colour.
- // next two are values parsed as floats.
- // fifth is either 'above','below', or 'none'.
- // sixth is a float value and only required when fifth is either
- // 'above' or 'below'.
- StringTokenizer gcol = new StringTokenizer(colscheme, "|",
- true);
- // set defaults
- int threshtype = AnnotationColourGradient.NO_THRESHOLD;
- float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
- boolean labelCol = false;
- // Parse spec line
- String mincol = gcol.nextToken();
- if (mincol == "|")
- {
- System.err
- .println("Expected either 'label' or a colour specification in the line: "
- + line);
- continue;
- }
- String maxcol = null;
- if (mincol.toLowerCase().indexOf("label") == 0)
- {
- labelCol = true;
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
- // '|'
- mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
- }
- String abso = null, minval, maxval;
- if (mincol != null)
- {
- // at least four more tokens
- if (mincol.equals("|"))
- {
- mincol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- // continue parsing rest of line
- maxcol = gcol.nextToken();
- if (maxcol.equals("|"))
- {
- maxcol = "";
- }
- else
- {
- gcol.nextToken(); // skip next '|'
- }
- abso = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- if (abso.toLowerCase().indexOf("abso") != 0)
- {
- minval = abso;
- abso = null;
- }
- else
- {
- minval = gcol.nextToken();
- gcol.nextToken(); // skip next '|'
- }
- maxval = gcol.nextToken();
- if (gcol.hasMoreTokens())
- {
- gcol.nextToken(); // skip next '|'
- }
- try
- {
- if (minval.length() > 0)
- {
- min = new Float(minval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the minimum value for graduated colour for type ("
- + colscheme
- + ") - did you misspell 'auto' for the optional automatic colour switch ?");
- e.printStackTrace();
- }
- try
- {
- if (maxval.length() > 0)
- {
- max = new Float(maxval).floatValue();
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the maximum value for graduated colour for type ("
- + colscheme + ")");
- e.printStackTrace();
- }
- }
- else
- {
- // add in some dummy min/max colours for the label-only
- // colourscheme.
- mincol = "FFFFFF";
- maxcol = "000000";
- }
- try
- {
- colour = new jalview.schemes.GraduatedColor(
- new UserColourScheme(mincol).findColour('A'),
- new UserColourScheme(maxcol).findColour('A'), min,
- max);
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse the graduated colour scheme ("
- + colscheme + ")");
- e.printStackTrace();
- }
- if (colour != null)
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setColourByLabel(labelCol);
- ((jalview.schemes.GraduatedColor) colour)
- .setAutoScaled(abso == null);
- // add in any additional parameters
- String ttype = null, tval = null;
- if (gcol.hasMoreTokens())
- {
- // threshold type and possibly a threshold value
- ttype = gcol.nextToken();
- if (ttype.toLowerCase().startsWith("below"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
- }
- else if (ttype.toLowerCase().startsWith("above"))
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
- }
- else
- {
- ((jalview.schemes.GraduatedColor) colour)
- .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
- if (!ttype.toLowerCase().startsWith("no"))
- {
- System.err
- .println("Ignoring unrecognised threshold type : "
- + ttype);
- }
- }
- }
- if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- try
- {
- gcol.nextToken();
- tval = gcol.nextToken();
- ((jalview.schemes.GraduatedColor) colour)
- .setThresh(new Float(tval).floatValue());
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse threshold value as a float: ("
- + tval + ")");
- e.printStackTrace();
- }
- }
- // parse the thresh-is-min token ?
- if (gcol.hasMoreTokens())
- {
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
- while (gcol.hasMoreTokens())
- {
- System.err.println("|" + gcol.nextToken());
- }
- System.err.println("\n");
- }
- }
- }
- else
- {
- UserColourScheme ucs = new UserColourScheme(colscheme);
- colour = ucs.findColour('A');
- }
- if (colour != null)
- {
- colours.put(type, colour);
- }
- if (st.hasMoreElements())
- {
- String link = st.nextToken();
- typeLink.put(type, link);
- if (featureLink == null)
- {
- featureLink = new Hashtable();
- }
- featureLink.put(type, link);
- }
- }
- continue;
- }
- String seqId = "";
- while (st.hasMoreElements())
- {
-
- if (GFFFile)
- {
- // Still possible this is an old Jalview file,
- // which does not have type colours at the beginning
- seqId = token = st.nextToken();
- seq = findName(align, seqId, relaxedIdmatching);
- if (seq != null)
- {
- desc = st.nextToken();
- String group = null;
- if (doGffSource && desc.indexOf(' ') == -1)
- {
- // could also be a source term rather than description line
- group = new String(desc);
- }
- type = st.nextToken();
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- start = 0;
- }
- else
- {
- start = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- start = 0;
- }
- try
- {
- String stt = st.nextToken();
- if (stt.length() == 0 || stt.equals("-"))
- {
- end = 0;
- }
- else
- {
- end = Integer.parseInt(stt);
- }
- } catch (NumberFormatException ex)
- {
- end = 0;
- }
- // TODO: decide if non positional feature assertion for input data
- // where end==0 is generally valid
- if (end == 0)
- {
- // treat as non-positional feature, regardless.
- start = 0;
- }
- try
- {
- score = new Float(st.nextToken()).floatValue();
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
-
- sf = new SequenceFeature(type, desc, start, end, score, group);
-
- try
- {
- sf.setValue("STRAND", st.nextToken());
- sf.setValue("FRAME", st.nextToken());
- } catch (Exception ex)
- {
- }
-
- if (st.hasMoreTokens())
- {
- StringBuffer attributes = new StringBuffer();
- while (st.hasMoreTokens())
- {
- attributes.append("\t" + st.nextElement());
- }
- // TODO validate and split GFF2 attributes field ? parse out
- // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
- // sf.setValue(attrib, val);
- sf.setValue("ATTRIBUTES", attributes.toString());
- }
-
- seq.addSequenceFeature(sf);
- while ((seq = align.findName(seq, seqId, true)) != null)
- {
- seq.addSequenceFeature(new SequenceFeature(sf));
- }
- break;
- }
- }
-
- if (GFFFile && seq == null)
- {
- desc = token;
- }
- else
- {
- desc = st.nextToken();
- }
- if (!st.hasMoreTokens())
- {
- System.err
- .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
- // in all probability, this isn't a file we understand, so bail
- // quietly.
- return false;
- }
-
- token = st.nextToken();
-
- if (!token.equals("ID_NOT_SPECIFIED"))
- {
- seq = findName(align, seqId = token, relaxedIdmatching);
- st.nextToken();
- }
- else
- {
- seqId = null;
- try
- {
- index = Integer.parseInt(st.nextToken());
- seq = align.getSequenceAt(index);
- } catch (NumberFormatException ex)
- {
- seq = null;
- }
- }
-
- if (seq == null)
- {
- System.out.println("Sequence not found: " + line);
- break;
- }
-
- start = Integer.parseInt(st.nextToken());
- end = Integer.parseInt(st.nextToken());
-
- type = st.nextToken();
-
- if (!colours.containsKey(type))
- {
- // Probably the old style groups file
- UserColourScheme ucs = new UserColourScheme(type);
- colours.put(type, ucs.findColour('A'));
- }
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
- if (st.hasMoreTokens())
- {
- try
- {
- score = new Float(st.nextToken()).floatValue();
- // update colourgradient bounds if allowed to
- } catch (NumberFormatException ex)
- {
- score = 0;
- }
- sf.setScore(score);
- }
- if (groupLink != null && removeHTML)
- {
- sf.addLink(groupLink);
- sf.description += "%LINK%";
- }
- if (typeLink.containsKey(type) && removeHTML)
- {
- sf.addLink(typeLink.get(type).toString());
- sf.description += "%LINK%";
- }
-
- parseDescriptionHTML(sf, removeHTML);
-
- seq.addSequenceFeature(sf);
-
- while (seqId != null
- && (seq = align.findName(seq, seqId, false)) != null)
- {
- seq.addSequenceFeature(new SequenceFeature(sf));
- }
- // If we got here, its not a GFFFile
- GFFFile = false;
- }
- }
- resetMatcher();
- } catch (Exception ex)
- {
- System.out.println(line);
- System.out.println("Error parsing feature file: " + ex + "\n" + line);
- ex.printStackTrace(System.err);
- resetMatcher();
- return false;
- }
-
- return true;
- }
-
- private AlignmentI lastmatchedAl = null;
-
- private SequenceIdMatcher matcher = null;
-
- /**
- * clear any temporary handles used to speed up ID matching
- */
- private void resetMatcher()
- {
- lastmatchedAl = null;
- matcher = null;
- }
-
- private SequenceI findName(AlignmentI align, String seqId,
- boolean relaxedIdMatching)
- {
- SequenceI match = null;
- if (relaxedIdMatching)
- {
- if (lastmatchedAl != align)
- {
- matcher = new SequenceIdMatcher(
- (lastmatchedAl = align).getSequencesArray());
- }
- match = matcher.findIdMatch(seqId);
- }
- else
- {
- match = align.findName(seqId, true);
- }
- return match;
- }
-
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
- {
- if (sf.getDescription() == null)
- {
- return;
- }
- jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
- sf.getDescription(), removeHTML, newline);
-
- sf.description = (removeHTML) ? parsed.getNonHtmlContent()
- : sf.description;
- for (String link : parsed.getLinks())
- {
- sf.addLink(link);
- }
-
- }
-
- /**
- * generate a features file for seqs includes non-pos features by default.
- *
- * @param seqs
- * source of sequence features
- * @param visible
- * hash of feature types and colours
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printJalviewFormat(seqs, visible, true, true);
- }
-
- /**
- * generate a features file for seqs with colours from visible (if any)
- *
- * @param seqs
- * source of features
- * @param visible
- * hash of Colours for each feature type
- * @param visOnly
- * when true only feature types in 'visible' will be output
- * @param nonpos
- * indicates if non-positional features should be output (regardless
- * of group or type)
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- boolean featuresGen = false;
- if (visOnly && !nonpos && (visible == null || visible.size() < 1))
- {
- // no point continuing.
- return "No Features Visible";
- }
-
- if (visible != null && visOnly)
- {
- // write feature colours only if we're given them and we are generating
- // viewed features
- // TODO: decide if feature links should also be written here ?
- Enumeration en = visible.keys();
- String type, color;
- while (en.hasMoreElements())
- {
- type = en.nextElement().toString();
-
- if (visible.get(type) instanceof GraduatedColor)
- {
- GraduatedColor gc = (GraduatedColor) visible.get(type);
- color = (gc.isColourByLabel() ? "label|" : "")
- + Format.getHexString(gc.getMinColor()) + "|"
- + Format.getHexString(gc.getMaxColor())
- + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
- + gc.getMax() + "|";
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
- {
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- color += "below";
- }
- else
- {
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- System.err.println("WARNING: Unsupported threshold type ("
- + gc.getThreshType() + ") : Assuming 'above'");
- }
- color += "above";
- }
- // add the value
- color += "|" + gc.getThresh();
- }
- else
- {
- color += "none";
- }
- }
- else if (visible.get(type) instanceof java.awt.Color)
- {
- color = Format.getHexString((java.awt.Color) visible.get(type));
- }
- else
- {
- // legacy support for integer objects containing colour triplet values
- color = Format.getHexString(new java.awt.Color(Integer
- .parseInt(visible.get(type).toString())));
- }
- out.append(type);
- out.append("\t");
- out.append(color);
- out.append(newline);
- }
- }
- // Work out which groups are both present and visible
- Vector groups = new Vector();
- int groupIndex = 0;
- boolean isnonpos = false;
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- if (next[j].featureGroup != null
- && !groups.contains(next[j].featureGroup))
- {
- groups.addElement(next[j].featureGroup);
- }
- }
- }
- }
-
- String group = null;
- do
- {
-
- if (groups.size() > 0 && groupIndex < groups.size())
- {
- group = groups.elementAt(groupIndex).toString();
- out.append(newline);
- out.append("STARTGROUP\t");
- out.append(group);
- out.append(newline);
- }
- else
- {
- group = null;
- }
-
- for (int i = 0; i < seqs.length; i++)
- {
- next = seqs[i].getSequenceFeatures();
- if (next != null)
- {
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- // skip if feature is nonpos and we ignore them or if we only
- // output visible and it isn't non-pos and it's not visible
- continue;
- }
-
- if (group != null
- && (next[j].featureGroup == null || !next[j].featureGroup
- .equals(group)))
- {
- continue;
- }
-
- if (group == null && next[j].featureGroup != null)
- {
- continue;
- }
- // we have features to output
- featuresGen = true;
- if (next[j].description == null
- || next[j].description.equals(""))
- {
- out.append(next[j].type + "\t");
- }
- else
- {
- if (next[j].links != null
- && next[j].getDescription().indexOf("<html>") == -1)
- {
- out.append("<html>");
- }
-
- out.append(next[j].description + " ");
- if (next[j].links != null)
- {
- for (int l = 0; l < next[j].links.size(); l++)
- {
- String label = next[j].links.elementAt(l).toString();
- String href = label.substring(label.indexOf("|") + 1);
- label = label.substring(0, label.indexOf("|"));
-
- if (next[j].description.indexOf(href) == -1)
- {
- out.append("<a href=\"" + href + "\">" + label + "</a>");
- }
- }
-
- if (next[j].getDescription().indexOf("</html>") == -1)
- {
- out.append("</html>");
- }
- }
-
- out.append("\t");
- }
- out.append(seqs[i].getName());
- out.append("\t-1\t");
- out.append(next[j].begin);
- out.append("\t");
- out.append(next[j].end);
- out.append("\t");
- out.append(next[j].type);
- if (next[j].score != Float.NaN)
- {
- out.append("\t");
- out.append(next[j].score);
- }
- out.append(newline);
- }
- }
- }
-
- if (group != null)
- {
- out.append("ENDGROUP\t");
- out.append(group);
- out.append(newline);
- groupIndex++;
- }
- else
- {
- break;
- }
-
- } while (groupIndex < groups.size() + 1);
-
- if (!featuresGen)
- {
- return "No Features Visible";
- }
-
- return out.toString();
- }
-
- /**
- * generate a gff file for sequence features includes non-pos features by
- * default.
- *
- * @param seqs
- * @param visible
- * @return
- */
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
- {
- return printGFFFormat(seqs, visible, true, true);
- }
-
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
- boolean visOnly, boolean nonpos)
- {
- StringBuffer out = new StringBuffer();
- SequenceFeature[] next;
- String source;
- boolean isnonpos;
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i].getSequenceFeatures() != null)
- {
- next = seqs[i].getSequenceFeatures();
- for (int j = 0; j < next.length; j++)
- {
- isnonpos = next[j].begin == 0 && next[j].end == 0;
- if ((!nonpos && isnonpos)
- || (!isnonpos && visOnly && !visible
- .containsKey(next[j].type)))
- {
- continue;
- }
-
- source = next[j].featureGroup;
- if (source == null)
- {
- source = next[j].getDescription();
- }
-
- out.append(seqs[i].getName());
- out.append("\t");
- out.append(source);
- out.append("\t");
- out.append(next[j].type);
- out.append("\t");
- out.append(next[j].begin);
- out.append("\t");
- out.append(next[j].end);
- out.append("\t");
- out.append(next[j].score);
- out.append("\t");
-
- if (next[j].getValue("STRAND") != null)
- {
- out.append(next[j].getValue("STRAND"));
- out.append("\t");
- }
- else
- {
- out.append(".\t");
- }
-
- if (next[j].getValue("FRAME") != null)
- {
- out.append(next[j].getValue("FRAME"));
- }
- else
- {
- out.append(".");
- }
- // TODO: verify/check GFF - should there be a /t here before attribute
- // output ?
-
- if (next[j].getValue("ATTRIBUTES") != null)
- {
- out.append(next[j].getValue("ATTRIBUTES"));
- }
-
- out.append(newline);
-
- }
- }
- }
-
- return out.toString();
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- */
- public void parse()
- {
- // IGNORED
- }
-
- /**
- * this is only for the benefit of object polymorphism - method does nothing.
- *
- * @return error message
- */
- public String print()
- {
- return "USE printGFFFormat() or printJalviewFormat()";
- }
-
-}
+package jalview.io;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+\r
+import jalview.analysis.SequenceIdMatcher;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+import jalview.util.Format;\r
+\r
+/**\r
+ * Parse and create Jalview Features files Detects GFF format features files and\r
+ * parses. Does not implement standard print() - call specific printFeatures or\r
+ * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object\r
+ * for the features annotation - this normally works on an exact match.\r
+ * \r
+ * @author AMW\r
+ * @version $Revision$\r
+ */\r
+public class FeaturesFile extends AlignFile\r
+{\r
+ /**\r
+ * work around for GFF interpretation bug where source string becomes\r
+ * description rather than a group\r
+ */\r
+ private boolean doGffSource = true;\r
+\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ */\r
+ public FeaturesFile()\r
+ {\r
+ }\r
+\r
+ /**\r
+ * Creates a new FeaturesFile object.\r
+ * \r
+ * @param inFile\r
+ * DOCUMENT ME!\r
+ * @param type\r
+ * DOCUMENT ME!\r
+ * \r
+ * @throws IOException\r
+ * DOCUMENT ME!\r
+ * @throws SAXException \r
+ * @throws ParserConfigurationException \r
+ * @throws ExceptionFileFormatOrSyntax \r
+ * @throws ExceptionLoadingFailed \r
+ * @throws ExceptionPermissionDenied \r
+ * @throws InterruptedException \r
+ * @throws ExceptionUnmatchedClosingParentheses \r
+ */\r
+ public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(source);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file using case-independent matching, discarding URLs\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param removeHTML - process html strings into plain text\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, Hashtable colours,\r
+ boolean removeHTML)\r
+ {\r
+ return parse(align, colours, null, removeHTML, false);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param removeHTML - process html strings into plain text\r
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, \r
+ Map colours, boolean removeHTML, boolean relaxedIdMatching)\r
+ {\r
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);\r
+ }\r
+\r
+ /**\r
+ * Parse GFF or sequence features file optionally using case-independent matching\r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align, Map colours,\r
+ Map featureLink, boolean removeHTML)\r
+ {\r
+ return parse(align, colours, featureLink, removeHTML, false);\r
+ }\r
+\r
+ /**\r
+ /**\r
+ * Parse GFF or sequence features file \r
+ * @param align - alignment/dataset containing sequences that are to be annotated\r
+ * @param colours - hashtable to store feature colour definitions\r
+ * @param featureLink - hashtable to store associated URLs \r
+ * @param removeHTML - process html strings into plain text\r
+ * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed\r
+ * @return true if features were added\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching)\r
+ {\r
+\r
+ String line = null;\r
+ try\r
+ {\r
+ SequenceI seq = null;\r
+ String type, desc, token = null;\r
+\r
+ int index, start, end;\r
+ float score;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ String featureGroup = null, groupLink = null;\r
+ Map typeLink = new Hashtable();\r
+ /**\r
+ * when true, assume GFF style features rather than Jalview style.\r
+ */\r
+ boolean GFFFile = true;\r
+ while ((line = nextLine()) != null)\r
+ {\r
+ if (line.startsWith("#"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 1)\r
+ {\r
+ if (line.trim().equalsIgnoreCase("GFF"))\r
+ {\r
+ // Start parsing file as if it might be GFF again.\r
+ GFFFile = true;\r
+ continue;\r
+ }\r
+ }\r
+ if (st.countTokens() > 1 && st.countTokens() < 4)\r
+ {\r
+ GFFFile = false;\r
+ type = st.nextToken();\r
+ if (type.equalsIgnoreCase("startgroup"))\r
+ {\r
+ featureGroup = st.nextToken();\r
+ if (st.hasMoreElements())\r
+ {\r
+ groupLink = st.nextToken();\r
+ featureLink.put(featureGroup, groupLink);\r
+ }\r
+ }\r
+ else if (type.equalsIgnoreCase("endgroup"))\r
+ {\r
+ // We should check whether this is the current group,\r
+ // but at present theres no way of showing more than 1 group\r
+ st.nextToken();\r
+ featureGroup = null;\r
+ groupLink = null;\r
+ }\r
+ else\r
+ {\r
+ Object colour = null;\r
+ String colscheme = st.nextToken();\r
+ if (colscheme.indexOf("|") > -1\r
+ || colscheme.trim().equalsIgnoreCase("label"))\r
+ {\r
+ // Parse '|' separated graduated colourscheme fields:\r
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]\r
+ // can either provide 'label' only, first is optional, next two\r
+ // colors are required (but may be\r
+ // left blank), next is optional, nxt two min/max are required.\r
+ // first is either 'label'\r
+ // first/second and third are both hexadecimal or word equivalent\r
+ // colour.\r
+ // next two are values parsed as floats.\r
+ // fifth is either 'above','below', or 'none'.\r
+ // sixth is a float value and only required when fifth is either\r
+ // 'above' or 'below'.\r
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",\r
+ true);\r
+ // set defaults\r
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;\r
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;\r
+ boolean labelCol = false;\r
+ // Parse spec line\r
+ String mincol = gcol.nextToken();\r
+ if (mincol == "|")\r
+ {\r
+ System.err\r
+ .println("Expected either 'label' or a colour specification in the line: "\r
+ + line);\r
+ continue;\r
+ }\r
+ String maxcol = null;\r
+ if (mincol.toLowerCase().indexOf("label") == 0)\r
+ {\r
+ labelCol = true;\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip\r
+ // '|'\r
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);\r
+ }\r
+ String abso = null, minval, maxval;\r
+ if (mincol != null)\r
+ {\r
+ // at least four more tokens\r
+ if (mincol.equals("|"))\r
+ {\r
+ mincol = "";\r
+ }\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ // continue parsing rest of line\r
+ maxcol = gcol.nextToken();\r
+ if (maxcol.equals("|"))\r
+ {\r
+ maxcol = "";\r
+ }\r
+ else\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ abso = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ if (abso.toLowerCase().indexOf("abso") != 0)\r
+ {\r
+ minval = abso;\r
+ abso = null;\r
+ }\r
+ else\r
+ {\r
+ minval = gcol.nextToken();\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ maxval = gcol.nextToken();\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ gcol.nextToken(); // skip next '|'\r
+ }\r
+ try\r
+ {\r
+ if (minval.length() > 0)\r
+ {\r
+ min = new Float(minval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the minimum value for graduated colour for type ("\r
+ + colscheme\r
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
+ e.printStackTrace();\r
+ }\r
+ try\r
+ {\r
+ if (maxval.length() > 0)\r
+ {\r
+ max = new Float(maxval).floatValue();\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the maximum value for graduated colour for type ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // add in some dummy min/max colours for the label-only\r
+ // colourscheme.\r
+ mincol = "FFFFFF";\r
+ maxcol = "000000";\r
+ }\r
+ try\r
+ {\r
+ colour = new jalview.schemes.GraduatedColor(\r
+ new UserColourScheme(mincol).findColour('A'),\r
+ new UserColourScheme(maxcol).findColour('A'), min,\r
+ max);\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse the graduated colour scheme ("\r
+ + colscheme + ")");\r
+ e.printStackTrace();\r
+ }\r
+ if (colour != null)\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setColourByLabel(labelCol);\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setAutoScaled(abso == null);\r
+ // add in any additional parameters\r
+ String ttype = null, tval = null;\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ // threshold type and possibly a threshold value\r
+ ttype = gcol.nextToken();\r
+ if (ttype.toLowerCase().startsWith("below"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);\r
+ }\r
+ else if (ttype.toLowerCase().startsWith("above"))\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);\r
+ }\r
+ else\r
+ {\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);\r
+ if (!ttype.toLowerCase().startsWith("no"))\r
+ {\r
+ System.err\r
+ .println("Ignoring unrecognised threshold type : "\r
+ + ttype);\r
+ }\r
+ }\r
+ }\r
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ try\r
+ {\r
+ gcol.nextToken();\r
+ tval = gcol.nextToken();\r
+ ((jalview.schemes.GraduatedColor) colour)\r
+ .setThresh(new Float(tval).floatValue());\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse threshold value as a float: ("\r
+ + tval + ")");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ // parse the thresh-is-min token ?\r
+ if (gcol.hasMoreTokens())\r
+ {\r
+ System.err\r
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");\r
+ while (gcol.hasMoreTokens())\r
+ {\r
+ System.err.println("|" + gcol.nextToken());\r
+ }\r
+ System.err.println("\n");\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme(colscheme);\r
+ colour = ucs.findColour('A');\r
+ }\r
+ if (colour != null)\r
+ {\r
+ colours.put(type, colour);\r
+ }\r
+ if (st.hasMoreElements())\r
+ {\r
+ String link = st.nextToken();\r
+ typeLink.put(type, link);\r
+ if (featureLink == null)\r
+ {\r
+ featureLink = new Hashtable();\r
+ }\r
+ featureLink.put(type, link);\r
+ }\r
+ }\r
+ continue;\r
+ }\r
+ String seqId = "";\r
+ while (st.hasMoreElements())\r
+ {\r
+\r
+ if (GFFFile)\r
+ {\r
+ // Still possible this is an old Jalview file,\r
+ // which does not have type colours at the beginning\r
+ seqId = token = st.nextToken();\r
+ seq = findName(align, seqId, relaxedIdmatching);\r
+ if (seq != null)\r
+ {\r
+ desc = st.nextToken();\r
+ String group = null;\r
+ if (doGffSource && desc.indexOf(' ') == -1)\r
+ {\r
+ // could also be a source term rather than description line\r
+ group = new String(desc);\r
+ }\r
+ type = st.nextToken();\r
+ try\r
+ {\r
+ String stt = st.nextToken();\r
+ if (stt.length() == 0 || stt.equals("-"))\r
+ {\r
+ start = 0;\r
+ }\r
+ else\r
+ {\r
+ start = Integer.parseInt(stt);\r
+ }\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ start = 0;\r
+ }\r
+ try\r
+ {\r
+ String stt = st.nextToken();\r
+ if (stt.length() == 0 || stt.equals("-"))\r
+ {\r
+ end = 0;\r
+ }\r
+ else\r
+ {\r
+ end = Integer.parseInt(stt);\r
+ }\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ end = 0;\r
+ }\r
+ // TODO: decide if non positional feature assertion for input data\r
+ // where end==0 is generally valid\r
+ if (end == 0)\r
+ {\r
+ // treat as non-positional feature, regardless.\r
+ start = 0;\r
+ }\r
+ try\r
+ {\r
+ score = new Float(st.nextToken()).floatValue();\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, start, end, score, group);\r
+\r
+ try\r
+ {\r
+ sf.setValue("STRAND", st.nextToken());\r
+ sf.setValue("FRAME", st.nextToken());\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (st.hasMoreTokens())\r
+ {\r
+ StringBuffer attributes = new StringBuffer();\r
+ while (st.hasMoreTokens())\r
+ {\r
+ attributes.append("\t" + st.nextElement());\r
+ }\r
+ // TODO validate and split GFF2 attributes field ? parse out\r
+ // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as\r
+ // sf.setValue(attrib, val);\r
+ sf.setValue("ATTRIBUTES", attributes.toString());\r
+ }\r
+\r
+ seq.addSequenceFeature(sf);\r
+ while ((seq = align.findName(seq, seqId, true)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (GFFFile && seq == null)\r
+ {\r
+ desc = token;\r
+ }\r
+ else\r
+ {\r
+ desc = st.nextToken();\r
+ }\r
+ if (!st.hasMoreTokens())\r
+ {\r
+ System.err\r
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
+ // in all probability, this isn't a file we understand, so bail\r
+ // quietly.\r
+ return false;\r
+ }\r
+\r
+ token = st.nextToken();\r
+\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ seq = findName(align, seqId = token, relaxedIdmatching);\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ seqId = null;\r
+ try\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ seq = align.getSequenceAt(index);\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ seq = null;\r
+ }\r
+ }\r
+\r
+ if (seq == null)\r
+ {\r
+ System.out.println("Sequence not found: " + line);\r
+ break;\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ type = st.nextToken();\r
+\r
+ if (!colours.containsKey(type))\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ colours.put(type, ucs.findColour('A'));\r
+ }\r
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
+ if (st.hasMoreTokens())\r
+ {\r
+ try\r
+ {\r
+ score = new Float(st.nextToken()).floatValue();\r
+ // update colourgradient bounds if allowed to\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ score = 0;\r
+ }\r
+ sf.setScore(score);\r
+ }\r
+ if (groupLink != null && removeHTML)\r
+ {\r
+ sf.addLink(groupLink);\r
+ sf.description += "%LINK%";\r
+ }\r
+ if (typeLink.containsKey(type) && removeHTML)\r
+ {\r
+ sf.addLink(typeLink.get(type).toString());\r
+ sf.description += "%LINK%";\r
+ }\r
+\r
+ parseDescriptionHTML(sf, removeHTML);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+ while (seqId != null\r
+ && (seq = align.findName(seq, seqId, false)) != null)\r
+ {\r
+ seq.addSequenceFeature(new SequenceFeature(sf));\r
+ }\r
+ // If we got here, its not a GFFFile\r
+ GFFFile = false;\r
+ }\r
+ }\r
+ resetMatcher();\r
+ } catch (Exception ex)\r
+ {\r
+ System.out.println(line);\r
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
+ ex.printStackTrace(System.err);\r
+ resetMatcher();\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ private AlignmentI lastmatchedAl = null;\r
+\r
+ private SequenceIdMatcher matcher = null;\r
+\r
+ /**\r
+ * clear any temporary handles used to speed up ID matching\r
+ */\r
+ private void resetMatcher()\r
+ {\r
+ lastmatchedAl = null;\r
+ matcher = null;\r
+ }\r
+\r
+ private SequenceI findName(AlignmentI align, String seqId,\r
+ boolean relaxedIdMatching)\r
+ {\r
+ SequenceI match = null;\r
+ if (relaxedIdMatching)\r
+ {\r
+ if (lastmatchedAl != align)\r
+ {\r
+ matcher = new SequenceIdMatcher(\r
+ (lastmatchedAl = align).getSequencesArray());\r
+ }\r
+ match = matcher.findIdMatch(seqId);\r
+ }\r
+ else\r
+ {\r
+ match = align.findName(seqId, true);\r
+ }\r
+ return match;\r
+ }\r
+\r
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ {\r
+ if (sf.getDescription() == null)\r
+ {\r
+ return;\r
+ }\r
+ jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline);\r
+\r
+ sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description;\r
+ for (String link:parsed.getLinks())\r
+ {\r
+ sf.addLink(link);\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * generate a features file for seqs includes non-pos features by default.\r
+ * \r
+ * @param seqs\r
+ * source of sequence features\r
+ * @param visible\r
+ * hash of feature types and colours\r
+ * @return features file contents\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ return printJalviewFormat(seqs, visible, true, true);\r
+ }\r
+\r
+ /**\r
+ * generate a features file for seqs with colours from visible (if any)\r
+ * \r
+ * @param seqs\r
+ * source of features\r
+ * @param visible\r
+ * hash of Colours for each feature type\r
+ * @param visOnly\r
+ * when true only feature types in 'visible' will be output\r
+ * @param nonpos\r
+ * indicates if non-positional features should be output (regardless\r
+ * of group or type)\r
+ * @return features file contents\r
+ */\r
+ public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly, boolean nonpos)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+ boolean featuresGen = false;\r
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))\r
+ {\r
+ // no point continuing.\r
+ return "No Features Visible";\r
+ }\r
+\r
+ if (visible != null && visOnly)\r
+ {\r
+ // write feature colours only if we're given them and we are generating\r
+ // viewed features\r
+ // TODO: decide if feature links should also be written here ?\r
+ Enumeration en = visible.keys();\r
+ String type, color;\r
+ while (en.hasMoreElements())\r
+ {\r
+ type = en.nextElement().toString();\r
+\r
+ if (visible.get(type) instanceof GraduatedColor)\r
+ {\r
+ GraduatedColor gc = (GraduatedColor) visible.get(type);\r
+ color = (gc.isColourByLabel() ? "label|" : "")\r
+ + Format.getHexString(gc.getMinColor()) + "|"\r
+ + Format.getHexString(gc.getMaxColor())\r
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"\r
+ + gc.getMax() + "|";\r
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)\r
+ {\r
+ color += "below";\r
+ }\r
+ else\r
+ {\r
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)\r
+ {\r
+ System.err.println("WARNING: Unsupported threshold type ("\r
+ + gc.getThreshType() + ") : Assuming 'above'");\r
+ }\r
+ color += "above";\r
+ }\r
+ // add the value\r
+ color += "|" + gc.getThresh();\r
+ }\r
+ else\r
+ {\r
+ color += "none";\r
+ }\r
+ }\r
+ else if (visible.get(type) instanceof java.awt.Color)\r
+ {\r
+ color = Format.getHexString((java.awt.Color) visible.get(type));\r
+ }\r
+ else\r
+ {\r
+ // legacy support for integer objects containing colour triplet values\r
+ color = Format.getHexString(new java.awt.Color(Integer\r
+ .parseInt(visible.get(type).toString())));\r
+ }\r
+ out.append(type);\r
+ out.append("\t");\r
+ out.append(color);\r
+ out.append(newline);\r
+ }\r
+ }\r
+ // Work out which groups are both present and visible\r
+ Vector groups = new Vector();\r
+ int groupIndex = 0;\r
+ boolean isnonpos = false;\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (next[j].featureGroup != null\r
+ && !groups.contains(next[j].featureGroup))\r
+ {\r
+ groups.addElement(next[j].featureGroup);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ String group = null;\r
+ do\r
+ {\r
+\r
+ if (groups.size() > 0 && groupIndex < groups.size())\r
+ {\r
+ group = groups.elementAt(groupIndex).toString();\r
+ out.append(newline);\r
+ out.append("STARTGROUP\t");\r
+ out.append(group);\r
+ out.append(newline);\r
+ }\r
+ else\r
+ {\r
+ group = null;\r
+ }\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ if (next != null)\r
+ {\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ // skip if feature is nonpos and we ignore them or if we only\r
+ // output visible and it isn't non-pos and it's not visible\r
+ continue;\r
+ }\r
+\r
+ if (group != null\r
+ && (next[j].featureGroup == null || !next[j].featureGroup\r
+ .equals(group)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (group == null && next[j].featureGroup != null)\r
+ {\r
+ continue;\r
+ }\r
+ // we have features to output\r
+ featuresGen = true;\r
+ if (next[j].description == null\r
+ || next[j].description.equals(""))\r
+ {\r
+ out.append(next[j].type + "\t");\r
+ }\r
+ else\r
+ {\r
+ if (next[j].links != null\r
+ && next[j].getDescription().indexOf("<html>") == -1)\r
+ {\r
+ out.append("<html>");\r
+ }\r
+\r
+ out.append(next[j].description + " ");\r
+ if (next[j].links != null)\r
+ {\r
+ for (int l = 0; l < next[j].links.size(); l++)\r
+ {\r
+ String label = next[j].links.elementAt(l).toString();\r
+ String href = label.substring(label.indexOf("|") + 1);\r
+ label = label.substring(0, label.indexOf("|"));\r
+\r
+ if (next[j].description.indexOf(href) == -1)\r
+ {\r
+ out.append("<a href=\"" + href + "\">" + label + "</a>");\r
+ }\r
+ }\r
+\r
+ if (next[j].getDescription().indexOf("</html>") == -1)\r
+ {\r
+ out.append("</html>");\r
+ }\r
+ }\r
+\r
+ out.append("\t");\r
+ }\r
+ out.append(seqs[i].getName());\r
+ out.append("\t-1\t");\r
+ out.append(next[j].begin);\r
+ out.append("\t");\r
+ out.append(next[j].end);\r
+ out.append("\t");\r
+ out.append(next[j].type);\r
+ if (next[j].score != Float.NaN)\r
+ {\r
+ out.append("\t");\r
+ out.append(next[j].score);\r
+ }\r
+ out.append(newline);\r
+ }\r
+ }\r
+ }\r
+\r
+ if (group != null)\r
+ {\r
+ out.append("ENDGROUP\t");\r
+ out.append(group);\r
+ out.append(newline);\r
+ groupIndex++;\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\r
+\r
+ } while (groupIndex < groups.size() + 1);\r
+\r
+ if (!featuresGen)\r
+ {\r
+ return "No Features Visible";\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ /**\r
+ * generate a gff file for sequence features includes non-pos features by\r
+ * default.\r
+ * \r
+ * @param seqs\r
+ * @param visible\r
+ * @return\r
+ */\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
+ {\r
+ return printGFFFormat(seqs, visible, true, true);\r
+ }\r
+\r
+ public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
+ boolean visOnly, boolean nonpos)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ SequenceFeature[] next;\r
+ String source;\r
+ boolean isnonpos;\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getSequenceFeatures() != null)\r
+ {\r
+ next = seqs[i].getSequenceFeatures();\r
+ for (int j = 0; j < next.length; j++)\r
+ {\r
+ isnonpos = next[j].begin == 0 && next[j].end == 0;\r
+ if ((!nonpos && isnonpos)\r
+ || (!isnonpos && visOnly && !visible\r
+ .containsKey(next[j].type)))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ source = next[j].featureGroup;\r
+ if (source == null)\r
+ {\r
+ source = next[j].getDescription();\r
+ }\r
+\r
+ out.append(seqs[i].getName());\r
+ out.append("\t");\r
+ out.append(source);\r
+ out.append("\t");\r
+ out.append(next[j].type);\r
+ out.append("\t");\r
+ out.append(next[j].begin);\r
+ out.append("\t");\r
+ out.append(next[j].end);\r
+ out.append("\t");\r
+ out.append(next[j].score);\r
+ out.append("\t");\r
+\r
+ if (next[j].getValue("STRAND") != null)\r
+ {\r
+ out.append(next[j].getValue("STRAND"));\r
+ out.append("\t");\r
+ }\r
+ else\r
+ {\r
+ out.append(".\t");\r
+ }\r
+\r
+ if (next[j].getValue("FRAME") != null)\r
+ {\r
+ out.append(next[j].getValue("FRAME"));\r
+ }\r
+ else\r
+ {\r
+ out.append(".");\r
+ }\r
+ // TODO: verify/check GFF - should there be a /t here before attribute\r
+ // output ?\r
+\r
+ if (next[j].getValue("ATTRIBUTES") != null)\r
+ {\r
+ out.append(next[j].getValue("ATTRIBUTES"));\r
+ }\r
+\r
+ out.append(newline);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ return out.toString();\r
+ }\r
+\r
+ /**\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ */\r
+ public void parse()\r
+ {\r
+ // IGNORED\r
+ }\r
+\r
+ /**\r
+ * this is only for the benefit of object polymorphism - method does nothing.\r
+ * \r
+ * @return error message\r
+ */\r
+ public String print()\r
+ {\r
+ return "USE printGFFFormat() or printJalviewFormat()";\r
+ }\r
+\r
+}\r
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import com.stevesoft.pat.*;
-import jalview.datamodel.*;
-
-// import org.apache.log4j.*;
-
-/**
- * This class is supposed to parse a Stockholm format file into Jalview There
- * are TODOs in this class: we do not know what the database source and version
- * is for the file when parsing the #GS= AC tag which associates accessions with
- * sequences. Database references are also not parsed correctly: a separate
- * reference string parser must be added to parse the database reference form
- * into Jalview's local representation.
- *
- * @author bsb at sanger.ac.uk
- * @version 0.3 + jalview mods
- *
- */
-public class StockholmFile extends AlignFile
-{
- // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");
-
- public StockholmFile()
- {
- }
-
- public StockholmFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
- public StockholmFile(FileParse source) throws IOException
- {
- super(source);
- }
-
- public void initData()
- {
- super.initData();
- }
-
- /**
- * Parse a file in Stockholm format into Jalview's data model. The file has to
- * be passed at construction time
- *
- * @throws IOException
- * If there is an error with the input file
- */
- public void parse() throws IOException
- {
- StringBuffer treeString = new StringBuffer();
- String treeName = null;
- // --------------- Variable Definitions -------------------
- String line;
- String version;
- // String id;
- Hashtable seqAnn = new Hashtable(); // Sequence related annotations
- Hashtable seqs = new Hashtable();
- Regex p, r, rend, s, x;
-
- // Temporary line for processing RNA annotation
- // String RNAannot = "";
-
- // ------------------ Parsing File ----------------------
- // First, we have to check that this file has STOCKHOLM format, i.e. the
- // first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
- if (!r.search(nextLine()))
- {
- throw new IOException(
- "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");
- }
- else
- {
- version = r.stringMatched(1);
- // logger.debug("Stockholm version: " + version);
- }
-
- // We define some Regexes here that will be used regularily later
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
- // id/from/to
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
-
- // Convert all bracket types to parentheses (necessary for passing to VARNA)
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
-
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
- rend.optimize();
- p.optimize();
- s.optimize();
- r.optimize();
- x.optimize();
- openparen.optimize();
- closeparen.optimize();
-
- while ((line = nextLine()) != null)
- {
- if (line.length() == 0)
- {
- continue;
- }
- if (rend.search(line))
- {
- // End of the alignment, pass stuff back
-
- this.noSeqs = seqs.size();
- // logger.debug("Number of sequences: " + this.noSeqs);
- Enumeration accs = seqs.keys();
- while (accs.hasMoreElements())
- {
- String acc = (String) accs.nextElement();
- // logger.debug("Processing sequence " + acc);
- String seq = (String) seqs.remove(acc);
- if (maxLength < seq.length())
- {
- maxLength = seq.length();
- }
- int start = 1;
- int end = -1;
- String sid = acc;
- /*
- * Retrieve hash of annotations for this accession Associate
- * Annotation with accession
- */
- Hashtable accAnnotations = null;
-
- if (seqAnn != null && seqAnn.containsKey(acc))
- {
- accAnnotations = (Hashtable) seqAnn.remove(acc);
- // TODO: add structures to sequence
- }
-
- // Split accession in id and from/to
- if (p.search(acc))
- {
- sid = p.stringMatched(1);
- start = Integer.parseInt(p.stringMatched(2));
- end = Integer.parseInt(p.stringMatched(3));
- }
- // logger.debug(sid + ", " + start + ", " + end);
-
- Sequence seqO = new Sequence(sid, seq, start, end);
- // Add Description (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DE"))
- {
- String desc = (String) accAnnotations.get("DE");
- seqO.setDescription((desc == null) ? "" : desc);
- }
- // Add DB References (if any)
- if (accAnnotations != null && accAnnotations.containsKey("DR"))
- {
- String dbr = (String) accAnnotations.get("DR");
- if (dbr != null && dbr.indexOf(";") > -1)
- {
- String src = dbr.substring(0, dbr.indexOf(";"));
- String acn = dbr.substring(dbr.indexOf(";") + 1);
- jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
- // seqO.addDBRef(dbref);
- }
- }
- if (accAnnotations != null && accAnnotations.containsKey("SS"))
- {
- Vector v = (Vector) accAnnotations.get("SS");
-
- for (int i = 0; i < v.size(); i++)
- {
- AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);
- seqO.addAlignmentAnnotation(an);
- // annotations.add(an);
- }
- }
-
- Hashtable features = null;
- // We need to adjust the positions of all features to account for gaps
- try
- {
- features = (Hashtable) accAnnotations.remove("features");
- } catch (java.lang.NullPointerException e)
- {
- // loggerwarn("Getting Features for " + acc + ": " +
- // e.getMessage());
- // continue;
- }
- // if we have features
- if (features != null)
- {
- int posmap[] = seqO.findPositionMap();
- Enumeration i = features.keys();
- while (i.hasMoreElements())
- {
- // TODO: parse out secondary structure annotation as annotation
- // row
- // TODO: parse out scores as annotation row
- // TODO: map coding region to core jalview feature types
- String type = i.nextElement().toString();
- Hashtable content = (Hashtable) features.remove(type);
- Enumeration j = content.keys();
- while (j.hasMoreElements())
- {
- String desc = j.nextElement().toString();
- String ns = content.get(desc).toString();
- char[] byChar = ns.toCharArray();
- for (int k = 0; k < byChar.length; k++)
- {
- char c = byChar[k];
- if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM
- // uses
- // '.'
- // for
- // feature
- // background
- {
- int new_pos = posmap[k]; // look up nearest seqeunce
- // position to this column
- SequenceFeature feat = new SequenceFeature(type, desc,
- new_pos, new_pos, 0f, null);
-
- seqO.addSequenceFeature(feat);
- }
- }
- }
-
- }
-
- }
- // garbage collect
-
- // logger.debug("Adding seq " + acc + " from " + start + " to " + end
- // + ": " + seq);
- this.seqs.addElement(seqO);
- }
- return; // finished parsing this segment of source
- }
- else if (!r.search(line))
- {
- // System.err.println("Found sequence line: " + line);
-
- // Split sequence in sequence and accession parts
- if (!x.search(line))
- {
- // logger.error("Could not parse sequence line: " + line);
- throw new IOException("Could not parse sequence line: " + line);
- }
- String ns = (String) seqs.get(x.stringMatched(1));
- if (ns == null)
- {
- ns = "";
- }
- ns += x.stringMatched(2);
-
- seqs.put(x.stringMatched(1), ns);
- }
- else
- {
- String annType = r.stringMatched(1);
- String annContent = r.stringMatched(2);
-
- // System.err.println("type:" + annType + " content: " + annContent);
-
- if (annType.equals("GF"))
- {
- /*
- * Generic per-File annotation, free text Magic features: #=GF NH
- * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier
- * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS
- *
- * Compulsory fields: ------------------
- *
- * AC Accession number: Accession number in form PFxxxxx.version or
- * PBxxxxxx. ID Identification: One word name for family. DE
- * Definition: Short description of family. AU Author: Authors of the
- * entry. SE Source of seed: The source suggesting the seed members
- * belong to one family. GA Gathering method: Search threshold to
- * build the full alignment. TC Trusted Cutoff: Lowest sequence score
- * and domain score of match in the full alignment. NC Noise Cutoff:
- * Highest sequence score and domain score of match not in full
- * alignment. TP Type: Type of family -- presently Family, Domain,
- * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM
- * Alignment Method The order ls and fs hits are aligned to the model
- * to build the full align. // End of alignment.
- *
- * Optional fields: ----------------
- *
- * DC Database Comment: Comment about database reference. DR Database
- * Reference: Reference to external database. RC Reference Comment:
- * Comment about literature reference. RN Reference Number: Reference
- * Number. RM Reference Medline: Eight digit medline UI number. RT
- * Reference Title: Reference Title. RA Reference Author: Reference
- * Author RL Reference Location: Journal location. PI Previous
- * identifier: Record of all previous ID lines. KW Keywords: Keywords.
- * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.
- * NL Location: Location of nested domains - sequence ID, start and
- * end of insert.
- *
- * Obsolete fields: ----------- AL Alignment method of seed: The
- * method used to align the seed members.
- */
- // Let's save the annotations, maybe we'll be able to do something
- // with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
- if (an.search(annContent))
- {
- if (an.stringMatched(1).equals("NH"))
- {
- treeString.append(an.stringMatched(2));
- }
- else if (an.stringMatched(1).equals("TN"))
- {
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (getTreeCount() + 1);
- }
- addNewickTree(treeName, treeString.toString());
- }
- treeName = an.stringMatched(2);
- treeString = new StringBuffer();
- }
- setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));
- }
- }
- else if (annType.equals("GS"))
- {
- // Generic per-Sequence annotation, free text
- /*
- * Pfam uses these features: Feature Description ---------------------
- * ----------- AC <accession> ACcession number DE <freetext>
- * DEscription DR <db>; <accession>; Database Reference OS <organism>
- * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)
- * LO <look> Look (Color, etc.)
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String content = s.stringMatched(3);
- // TODO: store DR in a vector.
- // TODO: store AC according to generic file db annotation.
- Hashtable ann;
- if (seqAnn.containsKey(acc))
- {
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- ann = new Hashtable();
- }
- ann.put(type, content);
- seqAnn.put(acc, ann);
- }
- else
- {
- throw new IOException("Error parsing " + line);
- }
- }
- else if (annType.equals("GC"))
- {
- // Generic per-Column annotation, exactly 1 char per column
- // always need a label.
- if (x.search(annContent))
- {
- // parse out and create alignment annotation directly.
- parseAnnotationRow(annotations, x.stringMatched(1),
- x.stringMatched(2));
- }
- }
- else if (annType.equals("GR"))
- {
- // Generic per-Sequence AND per-Column markup, exactly 1 char per
- // column
- /*
- * Feature Description Markup letters ------- -----------
- * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface
- * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane
- * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;
- * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in
- * or after) [0-2]
- */
- if (s.search(annContent))
- {
- String acc = s.stringMatched(1);
- String type = s.stringMatched(2);
- String seq = new String(s.stringMatched(3));
- String description = null;
- // Check for additional information about the current annotation
- // We use a simple string tokenizer here for speed
- StringTokenizer sep = new StringTokenizer(seq, " \t");
- description = sep.nextToken();
- if (sep.hasMoreTokens())
- {
- seq = sep.nextToken();
- }
- else
- {
- seq = description;
- description = new String();
- }
- // sequence id with from-to fields
-
- Hashtable ann;
- // Get an object with all the annotations for this sequence
- if (seqAnn.containsKey(acc))
- {
- // logger.debug("Found annotations for " + acc);
- ann = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- // logger.debug("Creating new annotations holder for " + acc);
- ann = new Hashtable();
- seqAnn.put(acc, ann);
- }
- // TODO test structure, call parseAnnotationRow with vector from
- // hashtable for specific sequence
- Hashtable features;
- // Get an object with all the content for an annotation
- if (ann.containsKey("features"))
- {
- // logger.debug("Found features for " + acc);
- features = (Hashtable) ann.get("features");
- }
- else
- {
- // logger.debug("Creating new features holder for " + acc);
- features = new Hashtable();
- ann.put("features", features);
- }
-
- Hashtable content;
- if (features.containsKey(this.id2type(type)))
- {
- // logger.debug("Found content for " + this.id2type(type));
- content = (Hashtable) features.get(this.id2type(type));
- }
- else
- {
- // logger.debug("Creating new content holder for " +
- // this.id2type(type));
- content = new Hashtable();
- features.put(this.id2type(type), content);
- }
- String ns = (String) content.get(description);
- if (ns == null)
- {
- ns = "";
- }
- ns += seq;
- content.put(description, ns);
-
- if (type.equals("SS"))
- {
- Hashtable strucAnn;
- if (seqAnn.containsKey(acc))
- {
- strucAnn = (Hashtable) seqAnn.get(acc);
- }
- else
- {
- strucAnn = new Hashtable();
- }
-
- Vector newStruc = new Vector();
- parseAnnotationRow(newStruc, type, ns);
-
- strucAnn.put(type, newStruc);
- seqAnn.put(acc, strucAnn);
- }
- }
- else
- {
- System.err
- .println("Warning - couldn't parse sequence annotation row line:\n"
- + line);
- // throw new IOException("Error parsing " + line);
- }
- }
- else
- {
- throw new IOException("Unknown annotation detected: " + annType
- + " " + annContent);
- }
- }
- }
- if (treeString.length() > 0)
- {
- if (treeName == null)
- {
- treeName = "Tree " + (1 + getTreeCount());
- }
- addNewickTree(treeName, treeString.toString());
- }
- }
-
- protected static AlignmentAnnotation parseAnnotationRow(
- Vector annotation, String label, String annots)
- {
- String convert1, convert2 = null;
-
- // Convert all bracket types to parentheses
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
-
- // Detect if file is RNA by looking for bracket types
- Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
-
- convert1 = openparen.replaceAll(annots);
- convert2 = closeparen.replaceAll(convert1);
- annots = convert2;
-
- String type = (label.indexOf("_cons") == label.length() - 5) ? label
- .substring(0, label.length() - 5) : label;
- boolean ss = false;
- type = id2type(type);
- if (type.equals("secondary structure"))
- {
- ss = true;
- }
- // decide on secondary structure or not.
- Annotation[] els = new Annotation[annots.length()];
- for (int i = 0; i < annots.length(); i++)
- {
- String pos = annots.substring(i, i + 1);
- Annotation ann;
- ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- // be written out
- if (ss)
- {
- if (detectbrackets.search(pos))
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getRNASecStrucState(pos).charAt(0);
- }
- else
- {
- ann.secondaryStructure = jalview.schemes.ResidueProperties
- .getDssp3state(pos).charAt(0);
- }
-
- if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')
- {
- ann.displayCharacter = ""; // null; // " ";
- }
- else
- {
- ann.displayCharacter = " " + ann.displayCharacter;
- }
- }
-
- els[i] = ann;
- }
- AlignmentAnnotation annot = null;
- Enumeration e = annotation.elements();
- while (e.hasMoreElements())
- {
- annot = (AlignmentAnnotation) e.nextElement();
- if (annot.label.equals(type))
- break;
- annot = null;
- }
- if (annot == null)
- {
- annot = new AlignmentAnnotation(type, type, els);
- annotation.addElement(annot);
- }
- else
- {
- Annotation[] anns = new Annotation[annot.annotations.length
- + els.length];
- System.arraycopy(annot.annotations, 0, anns, 0,
- annot.annotations.length);
- System.arraycopy(els, 0, anns, annot.annotations.length, els.length);
- annot.annotations = anns;
- // System.out.println("else: ");
- }
- return annot;
- }
-
- public static String print(SequenceI[] s)
- {
- return "not yet implemented";
- }
-
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
- private static Hashtable typeIds = null;
- static
- {
- if (typeIds == null)
- {
- typeIds = new Hashtable();
- typeIds.put("SS", "secondary structure");
- typeIds.put("SA", "surface accessibility");
- typeIds.put("TM", "transmembrane");
- typeIds.put("PP", "posterior probability");
- typeIds.put("LI", "ligand binding");
- typeIds.put("AS", "active site");
- typeIds.put("IN", "intron");
- typeIds.put("IR", "interacting residue");
- typeIds.put("AC", "accession");
- typeIds.put("OS", "organism");
- typeIds.put("CL", "class");
- typeIds.put("DE", "description");
- typeIds.put("DR", "reference");
- typeIds.put("LO", "look");
- typeIds.put("RF", "reference positions");
-
- }
- }
-
- protected static String id2type(String id)
- {
- if (typeIds.containsKey(id))
- {
- return (String) typeIds.get(id);
- }
- System.err.println("Warning : Unknown Stockholm annotation type code "
- + id);
- return id;
- }
- /**
- * //ssline is complete secondary structure line private AlignmentAnnotation
- * addHelices(Vector annotation, String label, String ssline) {
- *
- * // decide on secondary structure or not. Annotation[] els = new
- * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {
- * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new
- * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
- *
- * ann.secondaryStructure =
- * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);
- *
- * ann.displayCharacter = "x" + ann.displayCharacter;
- *
- * System.out.println(ann.displayCharacter);
- *
- * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =
- * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =
- * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))
- * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =
- * new AlignmentAnnotation(type, type, els);
- * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new
- * Annotation[helicesAnnot.annotations.length + els.length];
- * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,
- * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,
- * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =
- * anns; }
- *
- * helicesAnnot.features = Rna.GetBasePairs(ssline);
- * Rna.HelixMap(helicesAnnot.features);
- *
- *
- * return helicesAnnot; }
- */
-}
+/*\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
++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
++ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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
++ * \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
+/*\r
+ * This extension was written by Benjamin Schuster-Boeckler at sanger.ac.uk\r
+ */\r
+package jalview.io;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+\r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import com.stevesoft.pat.*;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+import fr.orsay.lri.varna.factories.RNAFactory;\r
+import fr.orsay.lri.varna.models.rna.RNA;\r
+import jalview.datamodel.*;\r
+import jalview.analysis.Rna;\r
+\r
+// import org.apache.log4j.*;\r
+\r
+/**\r
+ * This class is supposed to parse a Stockholm format file into Jalview There\r
+ * are TODOs in this class: we do not know what the database source and version\r
+ * is for the file when parsing the #GS= AC tag which associates accessions with\r
+ * sequences. Database references are also not parsed correctly: a separate\r
+ * reference string parser must be added to parse the database reference form\r
+ * into Jalview's local representation.\r
+ * \r
+ * @author bsb at sanger.ac.uk\r
+ * @version 0.3 + jalview mods\r
+ * \r
+ */\r
+public class StockholmFile extends AlignFile\r
+{\r
+ // static Logger logger = Logger.getLogger("jalview.io.StockholmFile");\r
+ protected ArrayList<RNA> result;\r
+ public String id;\r
+ \r
+ public StockholmFile()\r
+ {\r
+ }\r
+\r
+ public StockholmFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public StockholmFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ super(source);\r
+ }\r
+\r
+ public void initData()\r
+ {\r
+ super.initData();\r
+ }\r
+\r
+ /**\r
+ * Parse a file in Stockholm format into Jalview's data model. The file has to\r
+ * be passed at construction time\r
+ * \r
+ * @throws IOException\r
+ * If there is an error with the input file\r
+ * @throws ExceptionUnmatchedClosingParentheses \r
+ */\r
+ public void parse() throws IOException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+ FileReader fr = null;\r
+ fr = new FileReader(inFile); \r
+\r
+ BufferedReader r = new BufferedReader (fr);\r
+ result = RNAFactory.loadSecStrStockholm(r);\r
+ System.out.println("this is the secondary scructure:" +result.size());\r
+ SequenceI[] seqs = new SequenceI[result.size()];\r
+ System.out.println(type); //the type is "File"\r
+ System.out.println(inFile );//inFile is the path\r
+ for(int i=0;i<result.size();i++)\r
+ {\r
+ RNA current = result.get(i);\r
+ \r
+ System.out.println(current.getSeq());\r
+ //System.out.println(result.get(i).getStructBPSEQ());\r
+ System.out.println(result.get(i).getStructDBN(true));\r
+ System.out.println(i);\r
+ String rna =current.getStructDBN(true);\r
+ String seq = current.getSeq();\r
+ int begin=0;\r
+ int end = seq.length()-1;\r
+ id = safeName(getDataName());\r
+ seqs[i] = new Sequence(id, seq, begin, end);\r
+ String[] annot=new String[rna.length()] ;\r
+ Annotation[] ann = new Annotation[rna.length()];\r
+ for(int j=0;j<rna.length();j++)\r
+ {\r
+ annot[j] =rna.substring(j,j+1);\r
+ \r
+ }\r
+ \r
+ for(int k=0;k<rna.length();k++)\r
+ {\r
+ ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);\r
+ \r
+ }\r
+ AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);\r
+ \r
+ seqs[i].addAlignmentAnnotation(align);\r
+ seqs[i].setRNA(result.get(i));\r
+ this.annotations.addElement(align);\r
+ }\r
+ this.setSeqs(seqs);\r
+ \r
+ }\r
+// r = new Regex("# STOCKHOLM ([\\d\\.]+)");\r
+ // if (!r.search(nextLine()))\r
+// {\r
+// throw new IOException(\r
+// "This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'");\r
+// }\r
+// else\r
+// {\r
+// version = r.stringMatched(1);\r
+// // logger.debug("Stockholm version: " + version);\r
+// }\r
+//\r
+// // We define some Regexes here that will be used regularily later\r
+// rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment\r
+// p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in\r
+// // id/from/to\r
+// s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype\r
+// r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line\r
+// x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence\r
+//\r
+// // Convert all bracket types to parentheses (necessary for passing to VARNA)\r
+// Regex openparen = new Regex("(<|\\[)", "(");\r
+// Regex closeparen = new Regex("(>|\\])", ")");\r
+//\r
+// // Detect if file is RNA by looking for bracket types\r
+// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+//\r
+// rend.optimize();\r
+// p.optimize();\r
+// s.optimize();\r
+// r.optimize();\r
+// x.optimize();\r
+// openparen.optimize();\r
+// closeparen.optimize();\r
+//\r
+// while ((line = nextLine()) != null)\r
+// {\r
+// if (line.length() == 0)\r
+// {\r
+// continue;\r
+// }\r
+// if (rend.search(line))\r
+// {\r
+// // End of the alignment, pass stuff back\r
+//\r
+// this.noSeqs = seqs.size();\r
+// // logger.debug("Number of sequences: " + this.noSeqs);\r
+// Enumeration accs = seqs.keys();\r
+// while (accs.hasMoreElements())\r
+// {\r
+// String acc = (String) accs.nextElement();\r
+// // logger.debug("Processing sequence " + acc);\r
+// String seq = (String) seqs.remove(acc);\r
+// if (maxLength < seq.length())\r
+// {\r
+// maxLength = seq.length();\r
+// }\r
+// int start = 1;\r
+// int end = -1;\r
+// String sid = acc;\r
+// /*\r
+// * Retrieve hash of annotations for this accession\r
+// * Associate Annotation with accession\r
+// */\r
+// Hashtable accAnnotations = null;\r
+//\r
+// if (seqAnn != null && seqAnn.containsKey(acc))\r
+// {\r
+// accAnnotations = (Hashtable) seqAnn.remove(acc);\r
+// //TODO: add structures to sequence\r
+// }\r
+//\r
+// // Split accession in id and from/to\r
+// if (p.search(acc))\r
+// {\r
+// sid = p.stringMatched(1);\r
+// start = Integer.parseInt(p.stringMatched(2));\r
+// end = Integer.parseInt(p.stringMatched(3));\r
+// }\r
+// // logger.debug(sid + ", " + start + ", " + end);\r
+//\r
+// Sequence seqO = new Sequence(sid, seq, start, end);\r
+// // Add Description (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DE"))\r
+// {\r
+// String desc = (String) accAnnotations.get("DE");\r
+// seqO.setDescription((desc == null) ? "" : desc);\r
+// }\r
+// // Add DB References (if any)\r
+// if (accAnnotations != null && accAnnotations.containsKey("DR"))\r
+// {\r
+// String dbr = (String) accAnnotations.get("DR");\r
+// if (dbr != null && dbr.indexOf(";") > -1)\r
+// {\r
+// String src = dbr.substring(0, dbr.indexOf(";"));\r
+// String acn = dbr.substring(dbr.indexOf(";") + 1);\r
+// jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+// // seqO.addDBRef(dbref);\r
+// }\r
+// } \r
+// if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
+// {\r
+// Vector v = (Vector) accAnnotations.get("SS");\r
+// \r
+// for (int i = 0; i < v.size(); i++)\r
+// {\r
+// AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
+// seqO.addAlignmentAnnotation(an);\r
+// //annotations.add(an);\r
+// }\r
+// }\r
+// \r
+// Hashtable features = null;\r
+// // We need to adjust the positions of all features to account for gaps\r
+// try\r
+// {\r
+// features = (Hashtable) accAnnotations.remove("features");\r
+// } catch (java.lang.NullPointerException e)\r
+// {\r
+// // loggerwarn("Getting Features for " + acc + ": " +\r
+// // e.getMessage());\r
+// // continue;\r
+// }\r
+// // if we have features\r
+// if (features != null)\r
+// {\r
+// int posmap[] = seqO.findPositionMap();\r
+// Enumeration i = features.keys();\r
+// while (i.hasMoreElements())\r
+// {\r
+// // TODO: parse out secondary structure annotation as annotation\r
+// // row\r
+// // TODO: parse out scores as annotation row\r
+// // TODO: map coding region to core jalview feature types\r
+// String type = i.nextElement().toString();\r
+// Hashtable content = (Hashtable) features.remove(type);\r
+// Enumeration j = content.keys();\r
+// while (j.hasMoreElements())\r
+// {\r
+// String desc = j.nextElement().toString();\r
+// String ns = content.get(desc).toString();\r
+// char[] byChar = ns.toCharArray();\r
+// for (int k = 0; k < byChar.length; k++)\r
+// {\r
+// char c = byChar[k];\r
+// if (!(c == ' ' || c == '_' || c == '-' || c == '.')) // PFAM\r
+// // uses\r
+// // '.'\r
+// // for\r
+// // feature\r
+// // background\r
+// {\r
+// int new_pos = posmap[k]; // look up nearest seqeunce\r
+// // position to this column\r
+// SequenceFeature feat = new SequenceFeature(type, desc,\r
+// new_pos, new_pos, 0f, null);\r
+//\r
+// seqO.addSequenceFeature(feat);\r
+// }\r
+// }\r
+// }\r
+//\r
+// }\r
+//\r
+// }\r
+// // garbage collect\r
+//\r
+// // logger.debug("Adding seq " + acc + " from " + start + " to " + end\r
+// // + ": " + seq);\r
+// this.seqs.addElement(seqO);\r
+// }\r
+// return; // finished parsing this segment of source\r
+// }\r
+// else if (!r.search(line))\r
+// {\r
+// // System.err.println("Found sequence line: " + line);\r
+//\r
+// // Split sequence in sequence and accession parts\r
+// if (!x.search(line))\r
+// {\r
+// // logger.error("Could not parse sequence line: " + line);\r
+// throw new IOException("Could not parse sequence line: " + line);\r
+// }\r
+// String ns = (String) seqs.get(x.stringMatched(1));\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += x.stringMatched(2);\r
+//\r
+// seqs.put(x.stringMatched(1), ns);\r
+// }\r
+// else\r
+// {\r
+// String annType = r.stringMatched(1);\r
+// String annContent = r.stringMatched(2);\r
+//\r
+// // System.err.println("type:" + annType + " content: " + annContent);\r
+//\r
+// if (annType.equals("GF"))\r
+// {\r
+// /*\r
+// * Generic per-File annotation, free text Magic features: #=GF NH\r
+// * <tree in New Hampshire eXtended format> #=GF TN <Unique identifier\r
+// * for the next tree> Pfam descriptions: 7. DESCRIPTION OF FIELDS\r
+// * \r
+// * Compulsory fields: ------------------\r
+// * \r
+// * AC Accession number: Accession number in form PFxxxxx.version or\r
+// * PBxxxxxx. ID Identification: One word name for family. DE\r
+// * Definition: Short description of family. AU Author: Authors of the\r
+// * entry. SE Source of seed: The source suggesting the seed members\r
+// * belong to one family. GA Gathering method: Search threshold to\r
+// * build the full alignment. TC Trusted Cutoff: Lowest sequence score\r
+// * and domain score of match in the full alignment. NC Noise Cutoff:\r
+// * Highest sequence score and domain score of match not in full\r
+// * alignment. TP Type: Type of family -- presently Family, Domain,\r
+// * Motif or Repeat. SQ Sequence: Number of sequences in alignment. AM\r
+// * Alignment Method The order ls and fs hits are aligned to the model\r
+// * to build the full align. // End of alignment.\r
+// * \r
+// * Optional fields: ----------------\r
+// * \r
+// * DC Database Comment: Comment about database reference. DR Database\r
+// * Reference: Reference to external database. RC Reference Comment:\r
+// * Comment about literature reference. RN Reference Number: Reference\r
+// * Number. RM Reference Medline: Eight digit medline UI number. RT\r
+// * Reference Title: Reference Title. RA Reference Author: Reference\r
+// * Author RL Reference Location: Journal location. PI Previous\r
+// * identifier: Record of all previous ID lines. KW Keywords: Keywords.\r
+// * CC Comment: Comments. NE Pfam accession: Indicates a nested domain.\r
+// * NL Location: Location of nested domains - sequence ID, start and\r
+// * end of insert.\r
+// * \r
+// * Obsolete fields: ----------- AL Alignment method of seed: The\r
+// * method used to align the seed members.\r
+// */\r
+// // Let's save the annotations, maybe we'll be able to do something\r
+// // with them later...\r
+// Regex an = new Regex("(\\w+)\\s*(.*)");\r
+// if (an.search(annContent))\r
+// {\r
+// if (an.stringMatched(1).equals("NH"))\r
+// {\r
+// treeString.append(an.stringMatched(2));\r
+// }\r
+// else if (an.stringMatched(1).equals("TN"))\r
+// {\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (getTreeCount() + 1);\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// treeName = an.stringMatched(2);\r
+// treeString = new StringBuffer();\r
+// }\r
+// setAlignmentProperty(an.stringMatched(1), an.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GS"))\r
+// {\r
+// // Generic per-Sequence annotation, free text\r
+// /*\r
+// * Pfam uses these features: Feature Description ---------------------\r
+// * ----------- AC <accession> ACcession number DE <freetext>\r
+// * DEscription DR <db>; <accession>; Database Reference OS <organism>\r
+// * OrganiSm (species) OC <clade> Organism Classification (clade, etc.)\r
+// * LO <look> Look (Color, etc.)\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String content = s.stringMatched(3);\r
+// // TODO: store DR in a vector.\r
+// // TODO: store AC according to generic file db annotation.\r
+// Hashtable ann;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// ann = new Hashtable();\r
+// }\r
+// ann.put(type, content);\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else if (annType.equals("GC"))\r
+// {\r
+// // Generic per-Column annotation, exactly 1 char per column\r
+// // always need a label.\r
+// if (x.search(annContent))\r
+// {\r
+// // parse out and create alignment annotation directly.\r
+// parseAnnotationRow(annotations, x.stringMatched(1),\r
+// x.stringMatched(2));\r
+// }\r
+// }\r
+// else if (annType.equals("GR"))\r
+// {\r
+// // Generic per-Sequence AND per-Column markup, exactly 1 char per\r
+// // column\r
+// /*\r
+// * Feature Description Markup letters ------- -----------\r
+// * -------------- SS Secondary Structure [HGIEBTSCX] SA Surface\r
+// * Accessibility [0-9X] (0=0%-10%; ...; 9=90%-100%) TM TransMembrane\r
+// * [Mio] PP Posterior Probability [0-9*] (0=0.00-0.05; 1=0.05-0.15;\r
+// * *=0.95-1.00) LI LIgand binding [*] AS Active Site [*] IN INtron (in\r
+// * or after) [0-2]\r
+// */\r
+// if (s.search(annContent))\r
+// {\r
+// String acc = s.stringMatched(1);\r
+// String type = s.stringMatched(2);\r
+// String seq = new String(s.stringMatched(3));\r
+// String description = null;\r
+// // Check for additional information about the current annotation\r
+// // We use a simple string tokenizer here for speed\r
+// StringTokenizer sep = new StringTokenizer(seq, " \t");\r
+// description = sep.nextToken();\r
+// if (sep.hasMoreTokens())\r
+// {\r
+// seq = sep.nextToken();\r
+// }\r
+// else\r
+// {\r
+// seq = description;\r
+// description = new String();\r
+// }\r
+// // sequence id with from-to fields\r
+//\r
+// Hashtable ann;\r
+// // Get an object with all the annotations for this sequence\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// // logger.debug("Found annotations for " + acc);\r
+// ann = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new annotations holder for " + acc);\r
+// ann = new Hashtable();\r
+// seqAnn.put(acc, ann);\r
+// }\r
+// //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
+// Hashtable features;\r
+// // Get an object with all the content for an annotation\r
+// if (ann.containsKey("features"))\r
+// {\r
+// // logger.debug("Found features for " + acc);\r
+// features = (Hashtable) ann.get("features");\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new features holder for " + acc);\r
+// features = new Hashtable();\r
+// ann.put("features", features);\r
+// }\r
+//\r
+// Hashtable content;\r
+// if (features.containsKey(this.id2type(type)))\r
+// {\r
+// // logger.debug("Found content for " + this.id2type(type));\r
+// content = (Hashtable) features.get(this.id2type(type));\r
+// }\r
+// else\r
+// {\r
+// // logger.debug("Creating new content holder for " +\r
+// // this.id2type(type));\r
+// content = new Hashtable();\r
+// features.put(this.id2type(type), content);\r
+// }\r
+// String ns = (String) content.get(description);\r
+// if (ns == null)\r
+// {\r
+// ns = "";\r
+// }\r
+// ns += seq;\r
+// content.put(description, ns);\r
+//
+// if(type.equals("SS")){\r
+// Hashtable strucAnn;\r
+// if (seqAnn.containsKey(acc))\r
+// {\r
+// strucAnn = (Hashtable) seqAnn.get(acc);\r
+// }\r
+// else\r
+// {\r
+// strucAnn = new Hashtable();\r
+// }\r
+// \r
+// Vector newStruc=new Vector();\r
+// parseAnnotationRow(newStruc, type,ns);\r
+// \r
+// strucAnn.put(type, newStruc);\r
+// seqAnn.put(acc, strucAnn);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// System.err\r
+// .println("Warning - couldn't parse sequence annotation row line:\n"\r
+// + line);\r
+// // throw new IOException("Error parsing " + line);\r
+// }\r
+// }\r
+// else\r
+// {\r
+// throw new IOException("Unknown annotation detected: " + annType\r
+// + " " + annContent);\r
+// }\r
+// }\r
+// }\r
+// if (treeString.length() > 0)\r
+// {\r
+// if (treeName == null)\r
+// {\r
+// treeName = "Tree " + (1 + getTreeCount());\r
+// }\r
+// addNewickTree(treeName, treeString.toString());\r
+// }\r
+// }\r
+//\r
+ protected static AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
+ String label, String annots)\r
+ {\r
+ String convert1, convert2 = null;\r
+\r
+ // Convert all bracket types to parentheses\r
+ Regex openparen = new Regex("(<|\\[)", "(");\r
+ Regex closeparen = new Regex("(>|\\])", ")");\r
+\r
+ // Detect if file is RNA by looking for bracket types\r
+ Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");\r
+\r
+ convert1 = openparen.replaceAll(annots);\r
+ convert2 = closeparen.replaceAll(convert1);\r
+ annots = convert2;\r
+\r
+ String type = (label.indexOf("_cons") == label.length() - 5) ? label\r
+ .substring(0, label.length() - 5) : label;\r
+ boolean ss = false;\r
+ type = id2type(type);\r
+ if (type.equals("secondary structure"))\r
+ {\r
+ ss = true;\r
+ }\r
+ // decide on secondary structure or not.\r
+ Annotation[] els = new Annotation[annots.length()];\r
+ for (int i = 0; i < annots.length(); i++)\r
+ {\r
+ String pos = annots.substring(i, i + 1);\r
+ Annotation ann;\r
+ ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
+ // be written out\r
+ if (ss)\r
+ {\r
+ if (detectbrackets.search(pos))\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getRNASecStrucState(pos).charAt(0);\r
+ }\r
+ else\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties\r
+ .getDssp3state(pos).charAt(0);\r
+ }\r
+\r
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0) == 'C')\r
+ {\r
+ ann.displayCharacter = ""; // null; // " ";\r
+ }\r
+ else\r
+ {\r
+ ann.displayCharacter = " " + ann.displayCharacter;\r
+ }\r
+ }\r
+\r
+ els[i] = ann;\r
+ }\r
+ AlignmentAnnotation annot = null;\r
+ Enumeration e = annotation.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ annot = (AlignmentAnnotation) e.nextElement();\r
+ if (annot.label.equals(type))\r
+ break;\r
+ annot = null;\r
+ }\r
+ if (annot == null)\r
+ {\r
+ annot = new AlignmentAnnotation(type, type, els);\r
+ annotation.addElement(annot);\r
+ }\r
+ else\r
+ {\r
+ Annotation[] anns = new Annotation[annot.annotations.length\r
+ + els.length];\r
+ System.arraycopy(annot.annotations, 0, anns, 0,\r
+ annot.annotations.length);\r
+ System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
+ annot.annotations = anns;\r
+ //System.out.println("else: ");\r
+ }\r
+ return annot;\r
+ }\r
+\r
+ public static String print(SequenceI[] s)\r
+ {\r
+ return "not yet implemented";\r
+ }\r
+\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ private static Hashtable typeIds = null;\r
+ static\r
+ {\r
+ if (typeIds == null)\r
+ {\r
+ typeIds = new Hashtable();\r
+ typeIds.put("SS", "secondary structure");\r
+ typeIds.put("SA", "surface accessibility");\r
+ typeIds.put("TM", "transmembrane");\r
+ typeIds.put("PP", "posterior probability");\r
+ typeIds.put("LI", "ligand binding");\r
+ typeIds.put("AS", "active site");\r
+ typeIds.put("IN", "intron");\r
+ typeIds.put("IR", "interacting residue");\r
+ typeIds.put("AC", "accession");\r
+ typeIds.put("OS", "organism");\r
+ typeIds.put("CL", "class");\r
+ typeIds.put("DE", "description");\r
+ typeIds.put("DR", "reference");\r
+ typeIds.put("LO", "look");\r
+ typeIds.put("RF", "reference positions");\r
+\r
+ }\r
+ }\r
+\r
+ protected static String id2type(String id)\r
+ {\r
+ if (typeIds.containsKey(id))\r
+ {\r
+ return (String) typeIds.get(id);\r
+ }\r
+ System.err.println("Warning : Unknown Stockholm annotation type code "\r
+ + id);\r
+ return id;\r
+ }\r
+ /**\r
+ * //ssline is complete secondary structure line private AlignmentAnnotation\r
+ * addHelices(Vector annotation, String label, String ssline) {\r
+ * \r
+ * // decide on secondary structure or not. Annotation[] els = new\r
+ * Annotation[ssline.length()]; for (int i = 0; i < ssline.length(); i++) {\r
+ * String pos = ssline.substring(i, i + 1); Annotation ann; ann = new\r
+ * Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not\r
+ * \r
+ * ann.secondaryStructure =\r
+ * jalview.schemes.ResidueProperties.getRNAssState(pos).charAt(0);\r
+ * \r
+ * ann.displayCharacter = "x" + ann.displayCharacter;\r
+ * \r
+ * System.out.println(ann.displayCharacter);\r
+ * \r
+ * els[i] = ann; } AlignmentAnnotation helicesAnnot = null; Enumeration e =\r
+ * annotation.elements(); while (e.hasMoreElements()) { helicesAnnot =\r
+ * (AlignmentAnnotation) e.nextElement(); if (helicesAnnot.label.equals(type))\r
+ * break; helicesAnnot = null; } if (helicesAnnot == null) { helicesAnnot =\r
+ * new AlignmentAnnotation(type, type, els);\r
+ * annotation.addElement(helicesAnnot); } else { Annotation[] anns = new\r
+ * Annotation[helicesAnnot.annotations.length + els.length];\r
+ * System.arraycopy(helicesAnnot.annotations, 0, anns, 0,\r
+ * helicesAnnot.annotations.length); System.arraycopy(els, 0, anns,\r
+ * helicesAnnot.annotations.length, els.length); helicesAnnot.annotations =\r
+ * anns; }\r
+ * \r
+ * helicesAnnot.features = Rna.GetBasePairs(ssline);\r
+ * Rna.HelixMap(helicesAnnot.features);\r
+ * \r
+ * \r
+ * return helicesAnnot; }\r
+ * \r
+ */\r
+ /**\r
+ * make a friendly ID string.\r
+ * \r
+ * @param dataName\r
+ * @return truncated dataName to after last '/'\r
+ */\r
+ private String safeName(String dataName)\r
+ {\r
+ int b = 0;\r
+ while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )\r
+ { \r
+ dataName = dataName.substring(b + 1).trim();\r
+ \r
+ }\r
+ int e = (dataName.length() - dataName.indexOf("."))+1;\r
+ dataName = dataName.substring(1,e).trim();\r
+ return dataName;\r
+ }\r
- }\r
++}
git://source.jalview.org / jalview.git / commitdiff