X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e146754bdb7c3a2fa0d50f90bdab25564c6983db;hb=09eebd8c6997a33049084e307078717cc1a693a6;hp=4f5b7d04ec17d18ee171ca8dc2de561fb1728ea1;hpb=2afaba8da802954edbedf5c0748412d965763a2c;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4f5b7d0..e146754 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -57,6 +57,7 @@ import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
@@ -150,6 +151,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
private MouseWheelListener[] _mwl;
+ private boolean notJustOne;
+
/**
* Creates a new AnnotationPanel object.
*
@@ -596,6 +599,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
else
{
+ GraphLine thr = aa[graphStretch].getThreshold();
int currentX = getColumnForXPos(evt.getX());
ContactListI forCurrentX = av.getContactList(aa[graphStretch],
currentX);
@@ -608,11 +612,48 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
int fr, to;
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
- for (int c = fr; c <= to; c++)
+ // select corresponding range in segment under mouse
{
- av.getColumnSelection().addElement(c);
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ av.getColumnSelection().addElement(currentX);
+ }
+ // and also select everything lower than the max range adjacent
+ // (kind of works)
+ {
+ int c = fr - 1;
+ ContactRange cr = forCurrentX.getRangeFor(fr, to);
+ double cval;
+ while (c > 0)
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= cr.getMax())
+ {
+ av.getColumnSelection().addElement(c--);
+ }
+ else
+ {
+ break;
+ }
+ }
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= cr.getMax())
+ {
+ av.getColumnSelection().addElement(c++);
+ }
+ else
+ {
+ break;
+ }
+ }
}
- av.getColumnSelection().addElement(currentX);
}
}
}
@@ -776,6 +817,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
* mostly vertical drag
*/
dragMode = DragMode.Resize;
+ notJustOne = evt.isShiftDown();
/*
* but could also be a matrix drag
@@ -816,7 +858,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
AlignmentAnnotation graphAnnotation = av.getAlignment()
.getAlignmentAnnotation()[graphStretch];
int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
- graphAnnotation.graphHeight = newHeight;
+ if (notJustOne)
+ {
+ for (AlignmentAnnotation similar : av.getAlignment()
+ .findAnnotations(null, graphAnnotation.getCalcId(),
+ graphAnnotation.label))
+ {
+ similar.graphHeight = newHeight;
+ }
+
+ }
+ else
+ {
+ graphAnnotation.graphHeight = newHeight;
+ }
adjustPanelHeight();
ap.paintAlignment(false, false);
}
@@ -889,29 +944,47 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
cma.graphHeight);
ContactGeometry.contactInterval lastXci = lastXcgeom
- .mapFor(rowIndex[1], rowIndex[1] + deltaY);
+ .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+
ContactGeometry cXcgeom = new ContactGeometry(forToX,
cma.graphHeight);
ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
- rowIndex[1] + deltaY);
+ rowIndex[1] - deltaY);
+
// mark rectangular region formed by drag
- System.err.println("Matrix Selection from last(" + lastXci.cStart
- + "," + lastXci.cEnd + ") to cur(" + cXci.cStart + ","
- + cXci.cEnd + ")");
+ System.err.println("Matrix Selection from last(" + fromXc + ",["
+ + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc
+ + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
int fr, to;
fr = Math.min(lastXci.cStart, lastXci.cEnd);
to = Math.max(lastXci.cStart, lastXci.cEnd);
System.err.println("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(c);
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(c);
+ av.getColumnSelection().addElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
fr = Math.min(cXci.cStart, cXci.cEnd);
to = Math.max(cXci.cStart, cXci.cEnd);
System.err.println("Marking " + fr + " to " + to);
for (int c = fr; c <= to; c++)
{
- av.getColumnSelection().addElement(c);
+ if (cma.sequenceRef != null)
+ {
+ int col = cma.sequenceRef.findIndex(c);
+ av.getColumnSelection().addElement(col);
+ }
+ else
+ {
+ av.getColumnSelection().addElement(c);
+ }
}
fr = Math.min(lastX, currentX);
to = Math.max(lastX, currentX);
@@ -1001,15 +1074,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
{
int[] res = new int[2];
+ res[0] = -1;
+ res[1] = 0;
if (aa == null)
{
- res[0] = -1;
- res[1] = 0;
return res;
}
int row = -1;
int height = 0, lheight = 0;
-
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
@@ -1080,14 +1152,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (clist != null)
{
ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
- ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
- rowAndOffset);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
- tooltip = "Contact from " + ci.cStart + " to " + ci.cEnd
- + "
Mean:" + cr.getMean();
-
- // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
- // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
+ tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ + " - " + ci.cEnd + "]" + "
Mean:" + cr.getMean();
+ int col = ann.sequenceRef.findPosition(column);
+ ap.getStructureSelectionManager()
+ .highlightPositionsOn(ann.sequenceRef, new int[][]
+ { new int[] { col, col },
+ new int[]
+ { ci.cStart, ci.cEnd } }, null);
}
}
return tooltip;
@@ -1249,24 +1323,37 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (image == null || imgWidth != image.getWidth(this)
|| image.getHeight(this) != getHeight())
{
- try
- {
- image = new BufferedImage(imgWidth,
- ap.getAnnotationPanel().getHeight(),
- BufferedImage.TYPE_INT_RGB);
- } catch (OutOfMemoryError oom)
+ boolean tried = false;
+ image = null;
+ while (image == null && !tried)
{
try
{
- System.gc();
- } catch (Exception x)
+ image = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ tried = true;
+ } catch (IllegalArgumentException exc)
+ {
+ System.err.println(
+ "Serious issue with viewport geometry imgWidth requested was "
+ + imgWidth);
+ return;
+ } catch (OutOfMemoryError oom)
{
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
}
- ;
- new OOMWarning(
- "Couldn't allocate memory to redraw screen. Please restart Jalview",
- oom);
- return;
+
}
gg = (Graphics2D) image.getGraphics();