-package jalview.gui;\r
-\r
-import jalview.jbgui.GAlignmentPanel;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.awt.print.*;\r
-\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
-{\r
-\r
- AlignViewport av;\r
- OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
- public AlignFrame alignFrame;\r
- ScalePanel scalePanel;\r
- ScorePanel scorePanel;\r
-\r
- public AlignmentPanel(AlignFrame af, AlignViewport av)\r
- {\r
- alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel (av, this);\r
- idPanel = new IdPanel (av, this);\r
- scalePanel = new ScalePanel(av, this);\r
- scorePanel = new ScorePanel(av);\r
-\r
- idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idPanel.addNotify();\r
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
- setScrollValues(0,0);\r
-\r
- hscroll.addAdjustmentListener(this);\r
- vscroll.addAdjustmentListener(this);\r
-\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- RefreshPanels();\r
- }\r
- });\r
- }\r
-\r
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\r
-\r
- // do we need to scroll the panel?\r
- if(results!=null && (av.getStartSeq()>results[0]\r
- || av.getEndSeq()<results[0]\r
- || av.getStartRes()>results[1]\r
- || av.getEndRes()<results[2]))\r
- setScrollValues(results[1], results[0]);\r
-\r
-\r
- }\r
-\r
-\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
-\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
-\r
-\r
- public void setGraphPanelVisible(boolean b)\r
- {\r
- scorePanelHolder.setVisible(b);\r
- idSpaceFillerPanel.setVisible(b);\r
- RefreshPanels();\r
- }\r
-\r
- public void setWrapAlignment(boolean wrap)\r
- {\r
- scalePanelHolder.setVisible(!wrap);\r
- scorePanelHolder.setVisible(!wrap);\r
-\r
- hscroll.setVisible(!wrap);\r
- idSpaceFillerPanel.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
- }\r
-\r
-\r
- public void setColourScheme()\r
- {\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if(av.getConservationSelected())\r
- {\r
-\r
- Alignment al = (Alignment)av.getAlignment();\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
-\r
- av.setGlobalColourScheme( ccs );\r
-\r
- }\r
- seqPanel.seqCanvas.paintFlag = true;\r
- repaint();\r
- }\r
- /*\r
- seqCanvas.paintFlag = true;\r
- if (av.getSelection().size() == 0)\r
- {\r
- seqCanvas.globalColorScheme = cs;\r
- for (int i = 0; i < av.alignment.getGroups().size();i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);\r
- sg.cs = cs;\r
- if(!showConservation\r
- && !(sg.cs instanceof Blosum62ColourScheme)\r
- && sg.cs instanceof ConservationColourScheme)\r
- {\r
- // remove ConservationColouring from existing Conservation group\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
- else if(showConservation && !(sg.cs instanceof ConservationColourScheme))\r
- {\r
- // add ConservationColouring to new group\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));\r
-\r
- if( isNewSelection(sg) )\r
- {\r
- sg = av.getAlignment().addGroup();\r
- for (int i=0; i < av.getSelection().size(); i++)\r
- {\r
- av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.\r
- sel.sequenceAt(i)),\r
- (Sequence) av.sel.sequenceAt(i));\r
- av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));\r
- }\r
- }\r
-\r
-\r
- sg.cs = cs;\r
-\r
- // Selection is made, we only want to change the conservationColour for selected group\r
- if( showConservation\r
- && !(sg.cs instanceof ConservationColourScheme)\r
- && !(sg.cs instanceof Blosum62ColourScheme))\r
- {\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
-\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
- }\r
- else if( !showConservation && sg.cs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
- }\r
- repaint();\r
- }\r
-\r
- boolean isNewSelection(SequenceGroup sg)\r
- {\r
- if(sg==null)\r
- return true;\r
-\r
- if(sg.getSize()!=av.getSelection().size())\r
- return true;\r
-\r
- for(int i=0; i<sg.getSize(); i++)\r
- if( !av.getSelection().contains( sg.getSequenceAt(i) ))\r
- return true;\r
-\r
- return false;\r
- }\r
-\r
-\r
- public ColourSchemeI getColourScheme()\r
- {\r
- if(av.getSelection().size()>0)\r
- return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;\r
- else\r
- return seqCanvas.globalColorScheme;\r
- }\r
-*/\r
-\r
-/* public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
- {\r
- seqPanel.setColourScheme(cs, conservation);\r
-\r
- av.setGlobalColourScheme(cs);\r
-\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
- }\r
-\r
- void updateResidueView()\r
- {\r
- if (viewport.getSelection().size() == 0)\r
- {\r
- for (int i = 0; i < viewport.alignment.getGroups().size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);\r
- sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );\r
- sg.setDisplayText( viewTextMenuItem.isSelected() );\r
- sg.setColourText( colourTextMenuItem.isSelected() );\r
- }\r
- }\r
- else\r
- {\r
- SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));\r
- if (alignPanel.seqPanel.isNewSelection(sg))\r
- {\r
- sg = viewport.getAlignment().addGroup();\r
- for (int i = 0; i < viewport.getSelection().size(); i++)\r
- {\r
- viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (\r
- Sequence) viewport.sel.sequenceAt(i)),\r
- (Sequence) viewport.sel.sequenceAt(\r
- i));\r
- viewport.alignment.addToGroup(sg,\r
- (Sequence) viewport.sel.sequenceAt(i));\r
- }\r
- }\r
-\r
- sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());\r
- sg.setDisplayText(viewTextMenuItem.isSelected());\r
- sg.setColourText(colourTextMenuItem.isSelected());\r
- }\r
- alignPanel.RefreshPanels();\r
- }*/\r
-\r
-\r
-\r
- public void RefreshPanels()\r
- {\r
- invalidate();\r
- seqPanel.seqCanvas.paintFlag = true;\r
- idPanel.idCanvas.paintFlag = true;\r
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- av.getConsensus(true);\r
- validate();\r
- repaint();\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
-\r
- }\r
-\r
- int hextent = 0;\r
- int vextent = 0;\r
-\r
- public void setScrollValues(int x, int y)\r
- {\r
- hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();\r
- vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
-\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
-\r
- if(vextent+y > av.getAlignment().getHeight())\r
- y = av.getAlignment().getHeight() - vextent;\r
-\r
- if(y<0)\r
- y = 0;\r
-\r
- if(x<0)\r
- x=0;\r
-\r
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
- repaint();\r
-\r
- }\r
-\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
-\r
- if (evt.getSource() == hscroll)\r
- {\r
- int x = hscroll.getValue();\r
- av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
- }\r
-\r
- if (evt.getSource() == vscroll)\r
- {\r
- int offy = vscroll.getValue();\r
- av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
- }\r
-\r
-\r
- if(overviewPanel!=null)\r
- overviewPanel.setBoxPosition();\r
-\r
- seqPanel.seqCanvas.paintFlag=true;\r
- repaint();\r
- }\r
-\r
-\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
- {\r
-\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
-\r
- int pwidth = (int)pf.getImageableWidth();\r
- int pheight = (int)pf.getImageableHeight();\r
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
-\r
- pg.setColor(Color.white);\r
- pg.fillRect(0,0,pwidth, pheight);\r
- pg.setFont( av.getFont() );\r
-\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- int totalRes = (pwidth - idWidth)/av.getCharWidth();\r
- int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;\r
- int pagesWide = av.getAlignment().getWidth() / totalRes +1;\r
- int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;\r
-\r
- if (pi >= pagesWide*pagesHigh)\r
- return Printable.NO_SUCH_PAGE;\r
-\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startRes, endRes, startSeq, endSeq;\r
- startRes = (pi % pagesWide) * totalRes;\r
- endRes = startRes + totalRes-1;\r
- if(endRes>av.getAlignment().getWidth())\r
- endRes = av.getAlignment().getWidth();\r
-\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
- if(endSeq > av.getAlignment().getHeight())\r
- endSeq = av.getAlignment().getHeight();\r
-\r
-\r
- ////////////////\r
- //draw Scale\r
- pg.translate(idWidth,0);\r
- scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
-\r
- pg.translate(-idWidth, 30);\r
- ////////////////\r
- // Draw the ids\r
- Color currentColor=null;\r
- Color currentTextColor=null;\r
- for(int i=startSeq; i<endSeq; i++)\r
- {\r
- if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
- {\r
- currentColor = Color.gray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
-\r
- pg.setColor(currentColor);\r
- pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
- idWidth,\r
- av.getCharHeight());\r
-\r
- pg.setColor(currentTextColor);\r
-\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));\r
- }\r
-\r
- // draw main sequence panel\r
- pg.translate(idWidth,0);\r
- pg.setClip(0,0,pwidth-idWidth, pheight);\r
- seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
-\r
- return Printable.PAGE_EXISTS;\r
- }\r
-\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Insets;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.List;
+
+import javax.swing.SwingUtilities;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.161 $
+ */
+public class AlignmentPanel extends GAlignmentPanel implements
+ AdjustmentListener, Printable, AlignmentViewPanel,
+ ViewportListenerI
+{
+ public AlignViewport av;
+
+ ViewportRanges vpRanges;
+
+ OverviewPanel overviewPanel;
+
+ private SeqPanel seqPanel;
+
+ private IdPanel idPanel;
+
+ private boolean headless;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ /** DOCUMENT ME!! */
+ public AlignFrame alignFrame;
+
+ private ScalePanel scalePanel;
+
+ private AnnotationPanel annotationPanel;
+
+ private AnnotationLabels alabels;
+
+ // this value is set false when selection area being dragged
+ boolean fastPaint = true;
+
+ private int hextent = 0;
+
+ private int vextent = 0;
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
+
+ private PropertyChangeListener propertyChangeListener;
+
+ private CalculationChooser calculationDialog;
+
+ /**
+ * Creates a new AlignmentPanel object.
+ *
+ * @param af
+ * @param av
+ */
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ alignFrame = af;
+ this.av = av;
+ vpRanges = av.getRanges();
+ setSeqPanel(new SeqPanel(av, this));
+ setIdPanel(new IdPanel(av, this));
+
+ setScalePanel(new ScalePanel(av, this));
+
+ idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+ setAnnotationPanel(new AnnotationPanel(this));
+ setAlabels(new AnnotationLabels(this));
+
+ annotationScroller.setViewportView(getAnnotationPanel());
+ annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
+
+ scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+ seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
+
+ setScrollValues(0, 0);
+
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
+ final AlignmentPanel ap = this;
+ propertyChangeListener = new PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
+ fontChanged();
+ adjustAnnotationHeight();
+ updateLayout();
+ }
+
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
+ alignFrame.updateEditMenuBar();
+
+ paintAlignment(true);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+ .getCharHeight() + fm.getDescent()));
+
+ getIdPanel().getIdCanvas().gg = null;
+ getSeqPanel().seqCanvas.img = null;
+ getAnnotationPanel().adjustPanelHeight();
+
+ Dimension d = calculateIdWidth();
+
+ d.setSize(d.width + 4, d.height);
+ getIdPanel().getIdCanvas().setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(d);
+
+ if (this.alignFrame.getSplitViewContainer() != null)
+ {
+ ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
+ }
+
+ repaint();
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth()
+ {
+ // calculate sensible default width when no preference is available
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
+ }
+
+ /**
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @param maxwidth
+ * -1 or maximum width allowed for IdWidth
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth(int maxwidth)
+ {
+ Container c = new Container();
+
+ FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
+ Font.ITALIC, av.font.getSize()));
+
+ AlignmentI al = av.getAlignment();
+ int i = 0;
+ int idWidth = 0;
+ String id;
+
+ while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
+ {
+ SequenceI s = al.getSequenceAt(i);
+
+ id = s.getDisplayId(av.getShowJVSuffix());
+
+ if (fm.stringWidth(id) > idWidth)
+ {
+ idWidth = fm.stringWidth(id);
+ }
+
+ i++;
+ }
+
+ // Also check annotation label widths
+ i = 0;
+
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
+
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
+
+ i++;
+ }
+ }
+
+ return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
+ idWidth), 12);
+ }
+
+ /**
+ * Highlight the given results on the alignment.
+ *
+ */
+ public void highlightSearchResults(SearchResultsI results)
+ {
+ scrollToPosition(results);
+ getSeqPanel().seqCanvas.highlightSearchResults(results);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
+ * @param results
+ */
+ public boolean scrollToPosition(SearchResultsI results)
+ {
+ return scrollToPosition(results, 0, true, false);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @param redrawOverview
+ * @return
+ */
+ public boolean scrollToPosition(SearchResultsI searchResults,
+ boolean redrawOverview)
+ {
+ return scrollToPosition(searchResults, 0, redrawOverview, false);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean redrawOverview, boolean centre)
+ {
+ int startv, endv, starts, ends;
+ // TODO: properly locate search results in view when large numbers of hidden
+ // columns exist before highlighted region
+ // do we need to scroll the panel?
+ // TODO: tons of nullpointerexceptions raised here.
+ if (results != null && results.getSize() > 0 && av != null
+ && av.getAlignment() != null)
+ {
+ int seqIndex = av.getAlignment().findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ int start = r[0];
+ int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+ - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ if (av.hasHiddenColumns())
+ {
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.findColumnPosition(start);
+ end = hidden.findColumnPosition(end);
+ if (start == end)
+ {
+ if (!hidden.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = vpRanges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
+ }
+ else if ((endv = vpRanges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
+ }
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
+ }
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ }
+ else
+ {
+ vpRanges.scrollToWrappedVisible(start);
+ }
+ }
+
+ paintAlignment(redrawOverview);
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param op
+ * DOCUMENT ME!
+ */
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ /**
+ *
+ * @param b
+ * Hide or show annotation panel
+ *
+ */
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.getWrapAlignment())
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationScroller.setVisible(b);
+ }
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ @Override
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ validateAnnotationDimensions(true);
+ addNotify();
+ paintAlignment(true);
+ }
+
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+
+ if (adjustPanelHeight)
+ {
+ int rowHeight = av.getCharHeight();
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar (as these are not laid out we can't inspect their
+ * actual heights). Insets gives frame borders.
+ */
+ int stuff = Platform.isAMac() ? 80 : 100;
+ Insets insets = alignFrame.getInsets();
+ int availableHeight = alignFrame.getHeight() - stuff - insets.top
+ - insets.bottom;
+
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
+ {
+ annotationHeight = Math.min(annotationHeight, availableHeight - 2
+ * rowHeight);
+ }
+ }
+ else
+ {
+ // maintain same window layout whilst updating sliders
+ annotationHeight = annotationScroller.getSize().height;
+ }
+ hscroll.addNotify();
+
+ annotationScroller.setPreferredSize(new Dimension(annotationScroller
+ .getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
+ annotationScroller.addNotify();
+ }
+
+ /**
+ * update alignment layout for viewport settings
+ *
+ * @param wrap
+ * DOCUMENT ME!
+ */
+ public void updateLayout()
+ {
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
+ vpRanges.setStartSeq(0);
+ scalePanelHolder.setVisible(!wrap);
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.isShowAnnotation())
+ {
+ annotationScroller.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
+
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+ .getCharHeight()) - 1;
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ repaint();
+ }
+
+
+ /**
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x
+ * visible column to scroll to
+ * @param y
+ * visible row to scroll to
+ *
+ */
+ public void setScrollValues(int xpos, int ypos)
+ {
+ int x = xpos;
+ int y = ypos;
+
+ if (av == null || av.getAlignment() == null)
+ {
+ return;
+ }
+
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
+ }
+ else
+ {
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
+
+ if (av.hasHiddenColumns())
+ {
+ // reset the width to exclude hidden columns
+ width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+ }
+
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
+
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
+ }
+
+ /**
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
+ *
+ * @param evt
+ * adjustment event encoding whether hscroll or vscroll changed
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.getViewportWidth();
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
+
+ if (av.getWrapAlignment())
+ {
+ if (evt.getSource() == hscroll)
+ {
+ return; // no horizontal scroll when wrapped
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+ int rowSize = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((offy * rowSize == oldX) && (oldwidth == rowSize))
+ {
+ return;
+ }
+ else if (offy > -1)
+ {
+ vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
+ }
+ }
+ else
+ {
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log
+ .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ vpRanges.setStartRes(0);
+ vpRanges.setStartSeq(0);
+ }
+ });
+ }
+ repaint();
+ }
+ else
+ {
+ // horizontal scroll
+ if (evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((y == oldY) && (height == oldheight))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndHeight(y, height);
+ }
+ if (!fastPaint)
+ {
+ repaint();
+ }
+ }
+ }
+
+ /**
+ * Repaint the alignment including the annotations and overview panels (if
+ * shown).
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
+ repaint();
+
+ if (updateOverview)
+ {
+ // TODO: determine if this paintAlignment changed structure colours
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ invalidate();
+
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ validate();
+
+ /*
+ * set scroll bar positions
+ */
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ }
+
+ /*
+ * Set vertical scroll bar parameters for wrapped panel
+ * @param res
+ * the residue to scroll to
+ */
+ private void setScrollingForWrappedPanel(int res)
+ {
+ // get the width of the alignment in residues
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
+
+ // get the width of the canvas in residues
+ int canvasWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ if (canvasWidth > 0)
+ {
+ // position we want to scroll to is number of canvasWidth's to get there
+ int current = res / canvasWidth;
+
+ // max scroll position: add one because extent is 1 and scrollbar value
+ // can only be set to at most max - extent
+ int max = maxwidth / canvasWidth + 1;
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(current, 1, 0, max);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ @Override
+ public int print(Graphics pg, PageFormat pf, int pi)
+ throws PrinterException
+ {
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
+
+ int pwidth = (int) pf.getImageableWidth();
+ int pheight = (int) pf.getImageableHeight();
+
+ if (av.getWrapAlignment())
+ {
+ return printWrappedAlignment(pwidth, pheight, pi, pg);
+ }
+ else
+ {
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * context.
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pi
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
+ * @throws PrinterException
+ */
+ public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+ Graphics idGraphics, Graphics alignmentGraphics)
+ throws PrinterException
+ {
+ final int idWidth = getVisibleIdWidth(false);
+
+ /*
+ * Get the horizontal offset to where we draw the sequences.
+ * This is idWidth if using a single Graphics context, else zero.
+ */
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int charHeight = av.getCharHeight();
+ int scaleHeight = charHeight + fm.getDescent();
+
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
+
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+
+ int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+
+ int alignmentWidth = av.getAlignment().getWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
+
+ final int startRes = (pi % pagesWide) * totalRes;
+ int endRes = (startRes + totalRes) - 1;
+
+ if (endRes > (alignmentWidth - 1))
+ {
+ endRes = alignmentWidth - 1;
+ }
+
+ final int startSeq = (pi / pagesWide) * totalSeq;
+ int endSeq = startSeq + totalSeq;
+
+ int alignmentHeight = av.getAlignment().getHeight();
+ if (endSeq > alignmentHeight)
+ {
+ endSeq = alignmentHeight;
+ }
+
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1)
+ * pageHeight;
+
+ if (av.isShowAnnotation())
+ {
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pageHeight;
+
+ if (pi >= (pagesWide * pagesHigh))
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
+ + 3;
+
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
+ Color currentColor = null;
+ Color currentTextColor = null;
+
+ SequenceI seq;
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ /*
+ * gray out ids of sequences in selection group (if any)
+ */
+ currentColor = Color.gray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
+ }
+
+ idGraphics.setColor(currentColor);
+ idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
+ charHeight);
+
+ idGraphics.setColor(currentTextColor);
+
+ int xPos = 0;
+ String displayId = seq.getDisplayId(av.getShowJVSuffix());
+ if (av.isRightAlignIds())
+ {
+ fm = idGraphics.getFontMetrics();
+ xPos = idWidth
+ - fm.stringWidth(displayId)
+ - 4;
+ }
+
+ idGraphics.drawString(displayId, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
+ }
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
+
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
+ startSeq, endSeq, 0);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
+ {
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
+
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ alignmentGraphics, -1, startRes, endRes + 1);
+ }
+
+ return Printable.PAGE_EXISTS;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
+ */
+ public int printWrappedAlignment(int pwidth, int pheight, int pi,
+ Graphics pg) throws PrinterException
+ {
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ + annotationHeight;
+
+ int idWidth = getVisibleIdWidth(false);
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
+
+ int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
+ - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ pg.setColor(Color.white);
+ pg.fillRect(0, 0, pwidth, pheight);
+ pg.setFont(av.getFont());
+
+ // //////////////
+ // Draw the ids
+ pg.setColor(Color.black);
+
+ pg.translate(0, -pi * pheight);
+
+ pg.setClip(0, pi * pheight, pwidth, pheight);
+
+ int ypos = hgap;
+
+ do
+ {
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ pg.setFont(getIdPanel().getIdCanvas().getIdfont());
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ String string = s.getDisplayId(av.getShowJVSuffix());
+ int xPos = 0;
+ if (av.isRightAlignIds())
+ {
+ FontMetrics fm = pg.getFontMetrics();
+ xPos = idWidth - fm.stringWidth(string) - 4;
+ }
+ pg.drawString(string, xPos,
+ ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+ - (av.getCharHeight() / 5));
+ }
+ if (labels != null)
+ {
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
+
+ pg.setFont(av.getFont());
+ labels.drawComponent(pg, idWidth);
+ pg.translate(
+ +3,
+ -ypos
+ - (av.getAlignment().getHeight() * av
+ .getCharHeight()));
+ }
+
+ ypos += cHeight;
+ } while (ypos < totalHeight);
+
+ pg.translate(idWidth, 0);
+
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
+
+ if ((pi * pheight) < totalHeight)
+ {
+ return Printable.PAGE_EXISTS;
+
+ }
+ else
+ {
+ return Printable.NO_SUCH_PAGE;
+ }
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @return
+ */
+ public int getVisibleIdWidth()
+ {
+ return getVisibleIdWidth(true);
+ }
+
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @param onscreen
+ * indicate if the Id width for onscreen or offscreen display should
+ * be returned
+ * @return
+ */
+ public int getVisibleIdWidth(boolean onscreen)
+ {
+ // see if rendering offscreen - check preferences and calc width accordingly
+ if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
+ {
+ return calculateIdWidth(-1).width + 4;
+ }
+ Integer idwidth = null;
+ if (onscreen
+ || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+ {
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
+ }
+ return idwidth.intValue() + 4;
+ }
+
+ void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+ {
+ int boarderBottomOffset = 5;
+ long pSessionId = System.currentTimeMillis();
+ headless = (System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true"));
+ if (alignFrame != null && !headless)
+ {
+ if (file != null)
+ {
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.saving_file", new Object[] { type.getLabel() }),
+ pSessionId);
+ }
+ }
+ try
+ {
+ AlignmentDimension aDimension = getAlignmentDimension();
+ try
+ {
+ jalview.util.ImageMaker im;
+ final String imageAction, imageTitle;
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ imageAction = "Create PNG image from alignment";
+ imageTitle = null;
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ imageAction = "Create EPS file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+ else
+ {
+ imageAction = "Create SVG file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+
+ im = new jalview.util.ImageMaker(this, type, imageAction,
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file, imageTitle,
+ alignFrame, pSessionId, headless);
+ Graphics graphics = im.getGraphics();
+ if (av.getWrapAlignment())
+ {
+ if (graphics != null)
+ {
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, 0,
+ graphics);
+ im.writeImage();
+ }
+ }
+ else
+ {
+ if (graphics != null)
+ {
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
+ 0, graphics, graphics);
+ im.writeImage();
+ }
+ }
+
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ } finally
+ {
+
+ }
+ }
+
+ public AlignmentDimension getAlignmentDimension()
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (headless)
+ {
+ // need to obtain default alignment width and then add in any
+ // additional allowance for id margin
+ // this duplicates the calculation in getWrappedHeight but adjusts for
+ // offscreen idWith
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right - getVisibleIdWidth()
+ + getVisibleIdWidth(false);
+ }
+ else
+ {
+ width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
+ }
+
+ }
+ else if (av.isShowAnnotation())
+ {
+ height += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+ return new AlignmentDimension(width, height);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makeEPS(File epsFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void makePNG(File pngFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
+ }
+
+ public void makeSVG(File svgFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+ }
+
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ {
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
+ int idWidth = getVisibleIdWidth(false);
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
+
+ // Gen image map
+ // ////////////////////////////////
+ if (imgMapFile != null)
+ {
+ try
+ {
+ int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
+ .getAlignment().getWidth(), g, gSize, f, fSize, sy;
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println("<img src=\"" + imageName
+ + "\" border=\"0\" usemap=\"#Map\" >"
+ + "<map name=\"Map\">");
+
+ for (s = 0; s < sSize; s++)
+ {
+ sy = s * av.getCharHeight() + scaleHeight;
+
+ SequenceI seq = av.getAlignment().getSequenceAt(s);
+ SequenceFeature[] features = seq.getSequenceFeatures();
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
+ for (res = 0; res < alwidth; res++)
+ {
+ StringBuilder text = new StringBuilder();
+ String triplet = null;
+ if (av.getAlignment().isNucleotide())
+ {
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(res) + "");
+ }
+ else
+ {
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ + "");
+ }
+
+ if (triplet == null)
+ {
+ continue;
+ }
+
+ int alIndex = seq.findPosition(res);
+ gSize = groups.length;
+ for (g = 0; g < gSize; g++)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
+ }
+
+ if (groups[g].getStartRes() < res
+ && groups[g].getEndRes() > res)
+ {
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
+ }
+ }
+
+ if (features != null)
+ {
+ if (text.length() < 1)
+ {
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
+ }
+ fSize = features.length;
+ for (f = 0; f < fSize; f++)
+ {
+
+ if ((features[f].getBegin() <= seq.findPosition(res))
+ && (features[f].getEnd() >= seq.findPosition(res)))
+ {
+ if (features[f].isContactFeature())
+ {
+ if (features[f].getBegin() == seq.findPosition(res)
+ || features[f].getEnd() == seq
+ .findPosition(res))
+ {
+ text.append("<br>").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
+ }
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(features[f].getType());
+ if (features[f].getDescription() != null
+ && !features[f].getType().equals(
+ features[f].getDescription()))
+ {
+ text.append(" ").append(features[f].getDescription());
+ }
+
+ if (features[f].getValue("status") != null)
+ {
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
+ }
+ }
+ }
+
+ }
+ }
+ if (text.length() > 1)
+ {
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
+ out.println(text.toString());
+ }
+ }
+ }
+ out.println("</map></body></html>");
+ out.close();
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ } // /////////END OF IMAGE MAP
+
+ }
+
+ int getWrappedHeight()
+ {
+ int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
+
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right;
+ }
+
+ int chunkWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(seqPanelWidth);
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int annotationHeight = 0;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ + annotationHeight;
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
+
+ int height = ((maxwidth / chunkWidth) + 1) * cHeight;
+
+ return height;
+ }
+
+ /**
+ * close the panel - deregisters all listeners and nulls any references to
+ * alignment data.
+ */
+ public void closePanel()
+ {
+ PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+ PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
+ PaintRefresher.RemoveComponent(this);
+
+ closeChildFrames();
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ }
+
+ if (av != null)
+ {
+ av.removePropertyChangeListener(propertyChangeListener);
+ jalview.structure.StructureSelectionManager ssm = av
+ .getStructureSelectionManager();
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ av.dispose();
+ av = null;
+ }
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.warn("Closing alignment panel which is already closed.");
+ }
+ }
+ }
+
+ /**
+ * Close any open dialogs that would be orphaned when this one is closed
+ */
+ protected void closeChildFrames()
+ {
+ if (calculationDialog != null)
+ {
+ calculationDialog.closeFrame();
+ }
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ updateAnnotation(applyGlobalSettings, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av == null ? null : av.getAlignment();
+ }
+
+ @Override
+ public String getViewName()
+ {
+ return av.viewName;
+ }
+
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ *
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try
+ {
+ if (alignFrame.getSplitViewContainer() != null)
+ {
+ /*
+ * bring enclosing SplitFrame to front first if there is one
+ */
+ ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
+ }
+ alignFrame.setSelected(b);
+ } catch (Exception ex)
+ {
+ }
+
+ if (b)
+ {
+ alignFrame.setDisplayedView(this);
+ }
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
+ }
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
+ {
+
+ return new FeatureRenderer(this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer()
+ {
+ return seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
+ {
+ fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
+ {
+ if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
+ {
+ getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
+ }
+ }
+
+ public ScalePanel getScalePanel()
+ {
+ return scalePanel;
+ }
+
+ public void setScalePanel(ScalePanel scalePanel)
+ {
+ this.scalePanel = scalePanel;
+ }
+
+ public SeqPanel getSeqPanel()
+ {
+ return seqPanel;
+ }
+
+ public void setSeqPanel(SeqPanel seqPanel)
+ {
+ this.seqPanel = seqPanel;
+ }
+
+ public AnnotationPanel getAnnotationPanel()
+ {
+ return annotationPanel;
+ }
+
+ public void setAnnotationPanel(AnnotationPanel annotationPanel)
+ {
+ this.annotationPanel = annotationPanel;
+ }
+
+ public AnnotationLabels getAlabels()
+ {
+ return alabels;
+ }
+
+ public void setAlabels(AnnotationLabels alabels)
+ {
+ this.alabels = alabels;
+ }
+
+ public IdPanel getIdPanel()
+ {
+ return idPanel;
+ }
+
+ public void setIdPanel(IdPanel idPanel)
+ {
+ this.idPanel = idPanel;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param verticalOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ public void scrollToCentre(SearchResultsI sr, int verticalOffset)
+ {
+ /*
+ * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+ * mapped), we can make the scroll-to location a sequence above the one
+ * actually mapped.
+ */
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue.
+ */
+ scrollToPosition(sr, verticalOffset, true, true);
+ }
+
+ /**
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setToScrollComplementPanel(boolean b)
+ {
+ this.scrollComplementaryPanel = b;
+ }
+
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
+ {
+ return this.scrollComplementaryPanel;
+ }
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ validateAnnotationDimensions(adjustHeight);
+ addNotify();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ paintAlignment(true);
+ }
+ else
+ {
+ // lightweight repaint
+ repaint();
+ }
+ }
+
+ @Override
+ /**
+ * Property change event fired when a change is made to the viewport ranges
+ * object associated with this alignment panel's viewport
+ */
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // update this panel's scroll values based on the new viewport ranges values
+ int x = vpRanges.getStartRes();
+ int y = vpRanges.getStartSeq();
+ setScrollValues(x, y);
+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment();
+ setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
+ {
+ calculationDialog = calculationChooser;
+ }
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff