/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.SearchResults;
+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 java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
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.print.PageFormat;
import javax.swing.SwingUtilities;
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-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;
-
/**
* DOCUMENT ME!
*
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
* true, suppresses invoking the same method recursively.
*/
- private boolean followingComplementScroll;
+ private boolean dontScrollComplement;
/**
* Creates a new AlignmentPanel object.
{
return av;
}
+
public void alignmentChanged()
{
av.alignmentChanged(this);
scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight()
- + fm.getDescent()));
+ .getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
*/
public boolean scrollToPosition(SearchResults results)
{
- return scrollToPosition(results, true, false);
+ return scrollToPosition(results, 0, true, false);
}
/**
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+ public boolean scrollToPosition(SearchResults searchResults,
+ boolean redrawOverview)
{
- return scrollToPosition(searchResults, redrawOverview, false);
+ return scrollToPosition(searchResults, 0, redrawOverview, false);
}
/**
* (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
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
- boolean redrawOverview, boolean centre)
+ 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 nullpointereexceptions raised here.
+ // TODO: tons of nullpointerexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
&& av.getAlignment() != null)
{
}
int start = r[0];
int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
// DEBUG
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
{
int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
- end = Math.min(end + offset, seq.getEnd() - 1);
+ end = end + offset - 1;
}
if (start < 0)
{
}
}
}
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+ // System.out.println("start=" + start + ", end=" + end + ", startv="
+ // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+ // + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
/*
* Scroll left to make start of search results visible
*/
- setScrollValues(start - 1, seqIndex);
+ // setScrollValues(start - 1, seqIndex); // plus one residue
+ setScrollValues(start, seqIndex);
}
else if ((endv = av.getEndRes()) <= end)
{
/*
* Scroll right to make end of search results visible
*/
- setScrollValues(startv + 1 + end - endv, seqIndex);
+ // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
+ setScrollValues(startv + end - endv, seqIndex);
}
else if ((starts = av.getStartSeq()) > seqIndex)
{
*/
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
- int height = getAnnotationPanel().adjustPanelHeight();
-
- int theight = av.getCharHeight()
- * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
- : av.getAlignment().getHiddenSequences().getSize()));
- float sscaling = (float) (theight / (1.0 * theight + height));
- float ascaling = (float) (height * 1.0 / alignFrame.getHeight());
- int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the applet. Need a better algorithm to
- // define behaviour
- // try and set height according to alignment
- if (ascaling > 0 && sscaling < 0.5)
- {
- // if the alignment is too big then
- // default is 0.5 split
- height = alignFrame.getHeight() / 2;
- }
- else
+ 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)
{
- // if space for more than one sequence row left when annotation is fully
- // displayed then set height to annotation height
- // otherwise, leave at least two lines of sequence shown.
- height = (rheight > av.getCharHeight()) ? height
- : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling)));
+ annotationHeight = Math.min(annotationHeight, availableHeight - 2
+ * rowHeight);
}
}
else
{
// maintain same window layout whilst updating sliders
- height = annotationScroller.getSize().height;
+ annotationHeight = annotationScroller.getSize().height;
}
hscroll.addNotify();
annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), height));
+ .getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), height));
- annotationScroller.validate();// repaint();
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
annotationScroller.addNotify();
}
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
- * visible column to scroll to DOCUMENT ME!
+ * visible column to scroll to
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll to "+x+","+y);
+ // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
x = 0;
}
+ /*
+ * each scroll adjustment triggers adjustmentValueChanged, which resets the
+ * 'do not scroll complement' flag; ensure it is the same for both
+ * operations
+ */
+ boolean flag = isDontScrollComplement();
hscroll.setValues(x, hextent, 0, width);
+ setDontScrollComplement(flag);
vscroll.setValues(y, vextent, 0, height);
}
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
* If there is one, scroll the (Protein/cDNA) complementary alignment to
* match, unless we are ourselves doing that.
*/
- if (isFollowingComplementScroll())
+ if (isDontScrollComplement())
{
- setFollowingComplementScroll(false);
+ setDontScrollComplement(false);
}
else
{
- av.scrollComplementaryAlignment(evt.getSource() == hscroll);
+ av.scrollComplementaryAlignment();
}
}
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment()
- .getAlignmentAnnotation(),
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
+ // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
+ /*
+ * set scroll bar positions; first suppress this being 'followed' in any
+ * complementary split pane
+ */
+ setDontScrollComplement(true);
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw main sequence panel
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+ endSeq, 0);
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
}
if (labels != null)
{
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
+ pg.translate(
+ +3,
+ -ypos
- (av.getAlignment().getHeight() * av
.getCharHeight()));
}
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[]
- { type.getLabel() }), progress);
+ "status.saving_file", new Object[] { type.getLabel() }),
+ progress);
}
try
{
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+ alignFrame.setProgressBar(
+ MessageManager.getString("status.export_complete"),
+ progress);
}
}
}
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
+
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res)
- + "");
+ .getCharAt(res) + "");
}
else
{
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
@Override
public AlignmentI getAlignment()
{
- return av.getAlignment();
+ return av == null ? null : av.getAlignment();
}
-
@Override
public String getViewName()
{
{
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)
{
return new FeatureRenderer(this);
}
- @Override
+
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
- public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
* @param sr
* holds mapped region(s) of this alignment that we are scrolling
* 'to'; may be modified for sequence offset by this method
- * @param seqOffset
+ * @param verticalOffset
* the number of visible sequences to show above the mapped region
- * @param horizontal
- * if true, horizontal scrolling, else vertical
*/
- public void scrollAsComplement(SearchResults sr, int seqOffset,
- boolean horizontal)
+ public void scrollToCentre(SearchResults sr, int verticalOffset)
{
/*
* To avoid jumpy vertical scrolling (if some sequences are gapped or not
* This is like AlignmentI.findIndex(seq) but here we are matching the
* dataset sequence not the aligned sequence
*/
- int sequenceIndex = 0;
boolean matched = false;
for (SequenceI seq : seqs)
{
matched = true;
break;
}
- sequenceIndex++;
}
if (!matched)
{
return; // failsafe, shouldn't happen
}
- sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
- sr.getResults().get(0)
- .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
/*
- * Scroll to position but centring the target residue. Also set a state flag
- * to prevent adjustmentValueChanged performing this recursively.
+ * Scroll to position but centring the target residue.
*/
- setFollowingComplementScroll(true);
- scrollToPosition(sr, true, true);
+ scrollToPosition(sr, verticalOffset, true, true);
}
/**
- * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
*
* @param b
*/
- protected void setFollowingComplementScroll(boolean b)
+ protected void setDontScrollComplement(boolean b)
{
- this.followingComplementScroll = b;
+ this.dontScrollComplement = b;
}
- protected boolean isFollowingComplementScroll()
+ protected boolean isDontScrollComplement()
{
- return this.followingComplementScroll;
+ return this.dontScrollComplement;
}
}
git://source.jalview.org / jalview.git / blobdiff