X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ccb3464852dc621b512ebd787bf1da0c71297972;hb=4a4a5ad26799d8bd157c210153beaf21045d0402;hp=65546556e218a42f45c4c4bb2f7bc80d46cf1294;hpb=608282e79f4dd02c92565235b7946265bdca847d;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 6554655..ccb3464 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,7 +25,7 @@ import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
@@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
public AlignViewport av;
+ ViewportRanges vpRanges;
+
OverviewPanel overviewPanel;
private SeqPanel seqPanel;
@@ -91,9 +94,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
// this value is set false when selection area being dragged
boolean fastPaint = true;
- int hextent = 0;
+ private int hextent = 0;
- int vextent = 0;
+ private int vextent = 0;
/*
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -103,6 +106,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
private PropertyChangeListener propertyChangeListener;
+ private CalculationChooser calculationDialog;
+
/**
* Creates a new AlignmentPanel object.
*
@@ -113,6 +118,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
alignFrame = af;
this.av = av;
+ vpRanges = av.getRanges();
setSeqPanel(new SeqPanel(av, this));
setIdPanel(new IdPanel(av, this));
@@ -297,7 +303,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
getSeqPanel().seqCanvas.highlightSearchResults(results);
@@ -309,7 +315,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*
* @param results
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
{
return scrollToPosition(results, 0, true, false);
}
@@ -322,7 +328,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults,
+ public boolean scrollToPosition(SearchResultsI searchResults,
boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
@@ -342,7 +348,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
* if true, try to centre the search results horizontally in the view
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ public boolean scrollToPosition(SearchResultsI results,
int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
@@ -377,7 +383,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
if (centre)
{
- int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
end = end + offset - 1;
}
@@ -413,7 +419,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
- if ((startv = av.getStartRes()) >= start)
+ if ((startv = vpRanges.getStartRes()) >= start)
{
/*
* Scroll left to make start of search results visible
@@ -421,7 +427,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// setScrollValues(start - 1, seqIndex); // plus one residue
setScrollValues(start, seqIndex);
}
- else if ((endv = av.getEndRes()) <= end)
+ else if ((endv = vpRanges.getEndRes()) <= end)
{
/*
* Scroll right to make end of search results visible
@@ -429,19 +435,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
// setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
setScrollValues(startv + end - endv, seqIndex);
}
- else if ((starts = av.getStartSeq()) > seqIndex)
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
{
/*
* Scroll up to make start of search results visible
*/
- setScrollValues(av.getStartRes(), seqIndex);
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
}
- else if ((ends = av.getEndSeq()) <= seqIndex)
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
{
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
}
/*
* Else results are already visible - no need to scroll
@@ -464,10 +471,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int cwidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ if (res < vpRanges.getStartRes()
+ || res >= (vpRanges.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
+ vpRanges.setStartRes(vscroll.getValue() * cwidth);
}
}
@@ -591,7 +599,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
fontChanged();
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
- av.startSeq = 0;
+ vpRanges.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
@@ -688,7 +696,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
@@ -698,12 +705,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (av.hasHiddenColumns())
{
+ // reset the width to exclude hidden columns
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
-
hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
@@ -737,6 +742,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
x = 0;
}
+ // update endRes after x has (possibly) been adjusted
+ vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
+
/*
* each scroll adjustment triggers adjustmentValueChanged, which resets the
* 'do not scroll complement' flag; ensure it is the same for both
@@ -757,14 +766,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getStartSeq();
if (evt.getSource() == hscroll)
{
int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
.getCharWidth())) - 1);
}
@@ -778,8 +787,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int rowSize = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- av.setStartRes(offy * rowSize);
- av.setEndRes((offy + 1) * rowSize);
+ vpRanges.setStartRes(offy * rowSize);
+ vpRanges.setEndRes((offy + 1) * rowSize);
}
else
{
@@ -791,16 +800,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
@Override
public void run()
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(),
+ vpRanges.getStartSeq());
}
});
}
}
else
{
- av.setStartSeq(offy);
- av.setEndSeq(offy
- + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+ vpRanges.setStartSeq(offy);
+ vpRanges.setEndSeq(offy
+ + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+ - 1);
}
}
@@ -809,8 +820,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = vpRanges.getStartRes() - oldX;
+ int scrollY = vpRanges.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint)
{
@@ -820,13 +831,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
{
- scrollX = av.endRes - av.startRes;
+ scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
{
- scrollX = av.startRes - av.endRes;
+ scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
}
if (scrollX != 0 || scrollY != 0)
@@ -926,7 +937,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
else
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
}
}
@@ -1062,7 +1073,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
+ 3;
/*
- * draw the Scale at horizontal offset, then reset to origin
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, 0);
getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
@@ -1071,7 +1082,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
/*
* Draw the sequence ids, offset for scale height,
- * then reset to origin
+ * then reset to top left (0, 0)
*/
idGraphics.translate(0, scaleHeight);
idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
@@ -1122,7 +1133,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
/*
* draw the sequences, offset for scale height, and id width (if using a
- * single graphics context), then reset to origin + scale height
+ * single graphics context), then reset to (0, scale height)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
@@ -1132,16 +1143,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (av.isShowAnnotation() && (endSeq == alignmentHeight))
{
/*
- * draw annotation labels, offset for current scroll position
- * then reset to origin + scale height
+ * 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 + alignmentDrawnHeight);
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
getAlabels().drawComponent(idGraphics, idWidth);
- idGraphics.translate(0, -offset - alignmentDrawnHeight);
+ idGraphics.translate(0, -alignmentDrawnHeight);
/*
- * draw the annotations
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
@@ -1296,8 +1310,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
@@ -1445,7 +1459,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
@@ -1459,7 +1473,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.getAlignment().getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("![](\"")
res)
{
- text.append("
" + groups[g].getName() + "");
+ text.append("
").append(groups[g].getName())
+ .append("");
}
}
@@ -1518,12 +1533,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
if (text.length() < 1)
{
- text.append("= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("
disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("
").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
@@ -1551,13 +1567,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}
@@ -1633,6 +1649,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+ closeChildFrames();
+
/*
* try to ensure references are nulled
*/
@@ -1664,6 +1682,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
/**
+ * 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()
@@ -1822,14 +1851,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
* @param verticalOffset
* the number of visible sequences to show above the mapped region
*/
- public void scrollToCentre(SearchResults sr, int verticalOffset)
+ 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.getResultSequence(0);
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
List seqs = av.getAlignment().getSequences();
/*
@@ -1870,4 +1899,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
return this.dontScrollComplement;
}
+
+ /**
+ * 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();
+ }
+ }
+
+ /**
+ * 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;
+ }
}