/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.analysis.AnnotationSorter;
-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 java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
+import java.util.List;
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!
*
int vextent = 0;
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean followingComplementScroll;
+
/**
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
setScrollValues(0, 0);
- setAnnotationVisible(av.getShowAnnotation());
-
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
});
fontChanged();
adjustAnnotationHeight();
-
+ updateLayout();
}
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
public void alignmentChanged()
{
av.alignmentChanged(this);
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+ scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+ .getCharHeight()
+ fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getAnnotationPanel().adjustPanelHeight();
Dimension d = calculateIdWidth();
+
d.setSize(d.width + 4, d.height);
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
{
overviewPanel.setBoxPosition();
}
+ if (this.alignFrame.getSplitViewContainer() != null)
+ {
+ ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
+ }
repaint();
}
public Dimension calculateIdWidth()
{
// calculate sensible default width when no preference is available
-
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20,
- Math.min(afwidth - 200, 2 * afwidth / 3));
- return calculateIdWidth(maxwidth);
+ 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;
}
/**
}
/**
- * scroll the view to show the position of the highlighted region in 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(SearchResults results)
{
- return scrollToPosition(results, true);
+ return scrollToPosition(results, true, false);
}
/**
- * scroll the view to show the position of the highlighted region in results
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @param redrawOverview
+ * @return
+ */
+ public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+ {
+ return scrollToPosition(searchResults, redrawOverview, false);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
* (if any)
*
* @param results
* @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(SearchResults results,
- boolean redrawOverview)
+ boolean redrawOverview, boolean centre)
{
- int startv, endv, starts, ends, width;
+ 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?
int end = r[1];
// System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
// DEBUG
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = Math.min(end + offset, seq.getEnd() - 1);
+ }
if (start < 0)
{
return false;
}
}
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
{
+ /*
+ * Scroll left to make start of search results visible
+ */
setScrollValues(start - 1, seqIndex);
}
else if ((endv = av.getEndRes()) <= end)
{
+ /*
+ * Scroll right to make end of search results visible
+ */
setScrollValues(startv + 1 + end - endv, seqIndex);
}
else if ((starts = av.getStartSeq()) > seqIndex)
{
+ /*
+ * Scroll up to make start of search results visible
+ */
setScrollValues(av.getStartRes(), seqIndex);
}
else if ((ends = av.getEndSeq()) <= seqIndex)
{
+ /*
+ * Scroll down to make end of search results visible
+ */
setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
}
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
*/
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationScroller.setVisible(b);
}
/**
- * DOCUMENT ME!
+ * update alignment layout for viewport settings
*
* @param wrap
* DOCUMENT ME!
*/
- public void setWrapAlignment(boolean wrap)
+ public void updateLayout()
{
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
av.startSeq = 0;
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
- hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
- vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
if (hextent > width)
{
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
-
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
getScalePanel().repaint();
- if (av.getShowAnnotation() && scrollX != 0)
+ if (av.isShowAnnotation() && scrollX != 0)
{
getAnnotationPanel().fastPaint(scrollX);
}
}
}
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isFollowingComplementScroll())
+ {
+ setFollowingComplementScroll(false);
+ }
+ else
+ {
+ av.scrollComplementaryAlignment(evt.getSource() == hscroll);
+ }
}
/**
{
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
pg.setColor(currentTextColor);
pg.drawString(
seq.getDisplayId(av.getShowJVSuffix()),
xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw annotation - need to offset for current scroll position
int offset = -getAlabels().getScrollOffset();
pg.translate(0, offset);
- pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+ + 3);
getAlabels().drawComponent(pg, idWidth);
pg.translate(idWidth + 3, 0);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
int pi) throws PrinterException
{
-
int annotationHeight = 0;
AnnotationLabels labels = null;
if (av.isShowAnnotation())
labels = new AnnotationLabels(av);
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int idWidth = getVisibleIdWidth(false);
xPos = idWidth - fm.stringWidth(string) - 4;
}
pg.drawString(string, xPos,
- ((i * av.charHeight) + ypos + av.charHeight)
- - (av.charHeight / 5));
+ ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+ - (av.getCharHeight() / 5));
}
if (labels != null)
{
pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.charHeight));
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
pg.translate(+3, -ypos
- - (av.getAlignment().getHeight() * av.charHeight));
+ - (av.getAlignment().getHeight() * av
+ .getCharHeight()));
}
ypos += cHeight;
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file",
- new String[]
+ "status.saving_file", new Object[]
{ type.getLabel() }), progress);
}
try
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
if (av.getWrapAlignment())
{
}
}
- else if (av.getShowAnnotation())
+ else if (av.isShowAnnotation())
{
height += getAnnotationPanel().adjustPanelHeight() + 3;
}
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
for (s = 0; s < sSize; s++)
{
- sy = s * av.charHeight + scaleHeight;
+ sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
- Object obj = null;
+ String triplet = null;
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(res)
+ "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ "");
}
- if (obj == null)
+ if (triplet == null)
{
continue;
}
- String triplet = obj.toString();
int alIndex = seq.findPosition(res);
gSize = groups.length;
for (g = 0; g < gSize; g++)
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + ","
+ + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + ","
+ + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
int chunkWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(seqPanelWidth);
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
int annotationHeight = 0;
annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int maxwidth = av.getAlignment().getWidth();
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
av.setAlignment(null);
av = null;
}
new OOMWarning(string, error, this);
}
- public FeatureRenderer cloneFeatureRenderer()
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
{
return new FeatureRenderer(this);
}
-
- public void updateFeatureRenderer(FeatureRenderer fr)
+ @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(FeatureRenderer fr)
+ public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
{
if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
{
{
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 seqOffset
+ * 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)
+ {
+ /*
+ * 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.getResultSequence(0);
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * 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)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ 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.
+ */
+ setFollowingComplementScroll(true);
+ scrollToPosition(sr, true, true);
+ }
+
+ /**
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setFollowingComplementScroll(boolean b)
+ {
+ this.followingComplementScroll = b;
+ }
+
+ protected boolean isFollowingComplementScroll()
+ {
+ return this.followingComplementScroll;
+ }
}
git://source.jalview.org / jalview.git / blobdiff