X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=92b9a5065cd1b64168b5eb2ffa4a4b0a40023d33;hb=6853a22b51420bcea0fe12932d8850ffb30d9844;hp=53f65d8bdd2e2baf0b664a6dd550d248878d5701;hpb=faa7925a6bfe13bf2ca5f2f2ac3c7afa3027828b;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
old mode 100755
new mode 100644
index 53f65d8..92b9a50
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,287 +1,1767 @@
-package jalview.gui;
-
-import jalview.jbgui.GAlignmentPanel;
-import java.awt.*;
-import java.awt.image.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
-{
-
- AlignViewport av;
- OverviewPanel overviewPanel;
- SeqPanel seqPanel;
- IdPanel idPanel;
- public AlignFrame alignFrame;
- ScalePanel scalePanel;
- ScorePanel scorePanel;
-
- public boolean groupEdit = false;
-
- public AlignmentPanel(AlignFrame af, AlignViewport av)
- {
- alignFrame = af;
- this.av = av;
- seqPanel = new SeqPanel (av, this);
- idPanel = new IdPanel (av, this);
- scalePanel = new ScalePanel(av);
- scorePanel = new ScorePanel(av);
-
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
- idPanel.addNotify();
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
- setScrollValues(0,0);
-
- hscroll.addAdjustmentListener(this);
- vscroll.addAdjustmentListener(this);
- selectAll(false);
-
- addComponentListener(new ComponentAdapter()
- {
- public void componentResized(ComponentEvent evt)
- {
- RefreshPanels();
- }
- });
-
- }
-
- public int countSelected()
- {
- return av.getSelection().size();
- }
-
- public void selectAll(boolean flag) {
- int i = 0;
- if (flag) {
- while (i < av.getAlignment().getHeight()) {
- if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
- av.getSelection().addElement(av.getAlignment().getSequenceAt(i));
- }
- i++;
- }
- } else {
- av.getSelection().clear();
- }
- }
-
- public OverviewPanel getOverviewPanel()
- {
- return overviewPanel;
- }
-
- public void setOverviewPanel(OverviewPanel op)
- {
- overviewPanel = op;
- }
-
-
- public void setGraphPanelVisible(boolean b)
- {
- scorePanelHolder.setVisible(b);
- idSpaceFillerPanel.setVisible(b);
- RefreshPanels();
- }
-
- public void setWrapAlignment(boolean wrap)
- {
-
- scalePanelHolder.setVisible(!wrap);
- scorePanelHolder.setVisible(!wrap);
-
- hscroll.setVisible(!wrap);
- idSpaceFillerPanel.setVisible(!wrap);
- idSpaceFillerPanel1.setVisible(!wrap);
-
- }
-
-
- public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
- {
- seqPanel.setColourScheme(cs, conservation);
- if(overviewPanel!=null)
- overviewPanel.updateOverviewImage();
- }
-
-
- public void RefreshPanels()
- {
- invalidate();
- validate();
- idPanel.idCanvas.paintFlag = true;
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
- seqPanel.seqCanvas.paintFlag = true;
- setScrollValues(av.getStartRes(), av.getStartSeq());
- av.getConsensus(true);
- repaint();
-
- if(overviewPanel!=null)
- overviewPanel.updateOverviewImage();
-
- }
-
- int hextent = 0;
- int vextent = 0;
-
- public void setScrollValues(int x, int y)
- {
- hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());
- vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
-
- if(hextent+x > av.getAlignment().getWidth())
- x = av.getAlignment().getWidth()- hextent;
-
- if(vextent+y > av.getAlignment().getHeight())
- y = av.getAlignment().getHeight() - vextent;
-
- if(y<0)
- y = 0;
-
- if(x<0)
- x=0;
-
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
- seqPanel.seqCanvas.paintFlag = true;
- repaint();
-
- }
-
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
-
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));
- }
-
- if (evt.getSource() == vscroll)
- {
- int offy = vscroll.getValue();
- av.setStartSeq(offy);
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
- }
-
-
- if(overviewPanel!=null)
- overviewPanel.setBoxPosition();
-
-
- repaint();
- }
-
-
- public int print(Graphics g, PageFormat pf, int pi) throws PrinterException
- {
-
- int pwidth = (int)pf.getImageableWidth();
- int pheight = (int)pf.getImageableHeight();
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
-
- BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);
- Graphics pg = printImage.getGraphics();
- pg.setColor(Color.white);
- pg.fillRect(0,0,pwidth, pheight);
- pg.setFont( av.getFont() );
-
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());
- int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
- int pagesWide = av.getAlignment().getWidth() / totalRes +1;
- int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
-
- if (pi >= pagesWide*pagesHigh)
- return Printable.NO_SUCH_PAGE;
-
- /////////////////////////////
- /// Only print these sequences and residues on this page
- int startRes, endRes, startSeq, endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = startRes + totalRes-1;
- if(endRes>av.getAlignment().getWidth())
- endRes = av.getAlignment().getWidth();
-
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
- if(endSeq > av.getAlignment().getHeight())
- endSeq = av.getAlignment().getHeight();
-
-
- ////////////////
- //draw Scale
- pg.translate(idWidth,0);
- scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
-
- pg.translate(-idWidth, 30);
- ////////////////
- // Draw the ids
- Color currentColor=null;
- Color currentTextColor=null;
- for(int i=startSeq; i.
+ * 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.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+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.Graphics2D;
+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;
+
+ 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;
+
+ 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;
+ 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
+ ViewportRanges ranges = av.getRanges();
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.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();
+
+ // no idea if we need to update structure
+ paintAlignment(true, 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()));
+ idwidthAdjuster.invalidate();
+ scalePanelHolder.invalidate();
+ 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);
+
+ 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)
+ {
+ boolean scrolled = scrollToPosition(results, 0, false);
+
+ boolean noFastPaint = scrolled && av.getWrapAlignment();
+
+ getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @return
+ */
+ public boolean scrollToPosition(SearchResultsI searchResults)
+ {
+ return scrollToPosition(searchResults, 0, false);
+ }
+
+ /**
+ * Scrolls the view (if necessary) to show the position of the first
+ * highlighted region in results (if any). Answers true if the view was
+ * scrolled, or false if no matched region was found, or it is already
+ * visible.
+ *
+ * @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
+ * @return
+ */
+ protected boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean centre)
+ {
+ int startv, endv, starts, ends;
+ ViewportRanges ranges = av.getRanges();
+
+ if (results == null || results.isEmpty() || av == null
+ || av.getAlignment() == null)
+ {
+ return false;
+ }
+ 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 = (ranges.getEndRes() - ranges.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.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(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);
+ boolean scrollNeeded = true;
+
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = ranges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
+ }
+ else if ((endv = ranges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
+ }
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), seqIndex);
+ }
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
+ + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ scrollNeeded = false;
+ }
+ else
+ {
+ scrollNeeded = ranges.scrollToWrappedVisible(start);
+ }
+
+ paintAlignment(false, false);
+
+ return scrollNeeded;
+ }
+
+ /**
+ * 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();
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, av.needToUpdateStructureViews());
+ }
+
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+
+ 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();
+ ViewportRanges ranges = av.getRanges();
+ ranges.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);
+ validateAnnotationDimensions(false);
+ }
+
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth());
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight());
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.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().getVisibleWidth();
+ int height = av.getAlignment().getHeight();
+
+ 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)
+ {
+ if (av.getWrapAlignment())
+ {
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
+ 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;
+ }
+ ranges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
+ 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;
+ }
+ ranges.setViewportStartAndHeight(y, height);
+ }
+ repaint();
+ }
+
+ /**
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
+ *
+ * @param evt
+ */
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
+ {
+ if (evt.getSource() == hscroll)
+ {
+ return; // no horizontal scroll when wrapped
+ }
+ final ViewportRanges ranges = av.getRanges();
+
+ if (evt.getSource() == vscroll)
+ {
+ int newY = vscroll.getValue();
+
+ /*
+ * 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
+ */
+ int oldX = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
+ {
+ return;
+ }
+ if (newY > -1)
+ {
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = ranges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ ranges.setViewportStartAndWidth(Math.max(0, newX), 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
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
+ }
+ });
+ }
+ repaint();
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
+ repaint();
+
+ if (updateStructures)
+ {
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ invalidate(); // needed so that the id width adjuster works correctly
+
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
+ idPanelHolder.setPreferredSize(d);
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+
+ validate(); // needed so that the id width adjuster works correctly
+
+ /*
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
+ */
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+ }
+
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
+ */
+ private void setScrollingForWrappedPanel(int topLeftColumn)
+ {
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
+
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
+ }
+
+ /**
+ * 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);
+ }
+ }
+
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * contexts.
+ *
+ * @param pageWidth
+ * in pixels
+ * @param pageHeight
+ * in pixels
+ * @param pageIndex
+ * (0, 1, ...)
+ * @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 pageIndex,
+ 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());
+ final int charHeight = av.getCharHeight();
+ final 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?
+ */
+ final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+
+ final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
+
+ final int startRes = (pageIndex % pagesWide) * totalRes;
+ final int endRes = Math.min(startRes + totalRes - 1,
+ alignmentWidth - 1);
+
+ final int startSeq = (pageIndex / pagesWide) * totalSeq;
+ final int alignmentHeight = av.getAlignment().getHeight();
+ final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
+
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
+
+ if (av.isShowAnnotation())
+ {
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+
+ pagesHigh /= pageHeight;
+
+ if (pageIndex >= (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);
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ List selection = av.getSelectionGroup() == null ? null
+ : av.getSelectionGroup().getSequences(null);
+ idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+ selection);
+
+ 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.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq - 1);
+ 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;
+ }
+
+ /**
+ * Prints one page of an alignment in wrapped mode. Returns
+ * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
+ * no page could be drawn (page number out of range).
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pageNumber
+ * (0, 1, ...)
+ * @param g
+ *
+ * @return
+ *
+ * @throws PrinterException
+ */
+ public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
+ Graphics g) throws PrinterException
+ {
+ int annotationHeight = 0;
+ if (av.isShowAnnotation())
+ {
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ }
+
+ 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().getVisibleWidth();
+
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pageWidth - idWidth);
+
+ int totalHeight = cHeight * (maxwidth / resWidth + 1);
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, pageWidth, pageHeight);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ /*
+ * method: print the whole wrapped alignment, but with a clip region that
+ * is restricted to the requested page; this supports selective print of
+ * single pages or ranges, (at the cost of some repeated processing in
+ * the 'normal' case, when all pages are printed)
+ */
+ g.translate(0, -pageNumber * pageHeight);
+
+ g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
+
+ /*
+ * draw sequence ids and annotation labels (if shown)
+ */
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
+
+ g.translate(idWidth, 0);
+
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
+ totalHeight, 0);
+
+ if ((pageNumber * pageHeight) < 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().getVisibleWidth();
+
+ 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 sSize = av.getAlignment().getHeight();
+ int alwidth = av.getAlignment().getWidth();
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
+ out.println(HTMLOutput.getImageMapHTML());
+ out.println(""
+ + "