import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import java.util.List;
import jalview.analysis.AnnotationSorter;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.bin.JalviewLite;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
public boolean scrollToPosition(SearchResults results,
boolean redrawOverview)
{
+ return scrollToPosition(results, 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)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview, boolean centre)
+ {
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
{
- if (av.applet.debug)
+ if (JalviewLite.debug)
{// DEBUG
System.out
.println("DEBUG: scroll didn't happen - results not within alignment : "
}
return false;
}
- if (av.applet.debug)
+ if (JalviewLite.debug)
{
// DEBUG
/*
}
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 = (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;
* av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
* seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
* setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
- *
- * /*
*/
- if ((av.getStartRes() > end)
- || (av.getEndRes() < start)
- || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
- {
- if (start > av.getAlignment().getWidth() - hextent)
- {
- start = av.getAlignment().getWidth() - hextent;
- if (start < 0)
- {
- start = 0;
- }
+ // below is scrolling logic up to Jalview 2.8.2
+ // if ((av.getStartRes() > end)
+ // || (av.getEndRes() < start)
+ // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ // {
+ // if (start > av.getAlignment().getWidth() - hextent)
+ // {
+ // start = av.getAlignment().getWidth() - hextent;
+ // if (start < 0)
+ // {
+ // start = 0;
+ // }
+ //
+ // }
+ // if (seqIndex > av.getAlignment().getHeight() - vextent)
+ // {
+ // seqIndex = av.getAlignment().getHeight() - vextent;
+ // if (seqIndex < 0)
+ // {
+ // seqIndex = 0;
+ // }
+ // }
+ // setScrollValues(start, seqIndex);
+ // }
+ // logic copied from jalview.gui.AlignmentPanel:
+ 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);
}
- if (seqIndex > av.getAlignment().getHeight() - vextent)
+ else if ((ends = av.getEndSeq()) <= seqIndex)
{
- seqIndex = av.getAlignment().getHeight() - vextent;
- if (seqIndex < 0)
- {
- seqIndex = 0;
- }
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
}
- // System.out.println("trying to scroll to: "+start+" "+seqIndex);
- setScrollValues(start, seqIndex);
- }/**/
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
}
sendViewPosition();
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isFollowingComplementScroll())
+ {
+ setFollowingComplementScroll(false);
+ }
+ else
+ {
+ AlignmentPanel ap = getComplementPanel();
+ av.scrollComplementaryAlignment(ap);
+ }
+
+ }
+
+ /**
+ * A helper method to return the AlignmentPanel in the other (complementary)
+ * half of a SplitFrame view. Returns null if not in a SplitFrame.
+ *
+ * @return
+ */
+ private AlignmentPanel getComplementPanel()
+ {
+ AlignmentPanel ap = null;
+ if (alignFrame != null)
+ {
+ SplitFrame sf = alignFrame.getSplitFrame();
+ if (sf != null)
+ {
+ AlignFrame other = sf.getComplement(alignFrame);
+ if (other != null)
+ {
+ ap = other.alignPanel;
+ }
+ }
+ }
+ return ap;
+ }
+
+ /**
+ * 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
+ */
+ protected void scrollToCentre(SearchResults sr, int seqOffset)
+ {
+ /*
+ * 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);
}
private void sendViewPosition()
protected Panel seqPanelHolder = new Panel();
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
-
protected Panel scalePanelHolder = new Panel();
protected Panel idPanelHolder = new Panel();
- BorderLayout borderLayout5 = new BorderLayout();
-
protected Panel idSpaceFillerPanel1 = new Panel();
public Panel annotationSpaceFillerHolder = new Panel();
- BorderLayout borderLayout6 = new BorderLayout();
-
- BorderLayout borderLayout7 = new BorderLayout();
-
- Panel hscrollHolder = new Panel();
-
- BorderLayout borderLayout10 = new BorderLayout();
-
protected Panel hscrollFillerPanel = new Panel();
- BorderLayout borderLayout11 = new BorderLayout();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
Panel annotationPanelHolder = new Panel();
protected Scrollbar apvscroll = new Scrollbar();
- BorderLayout borderLayout12 = new BorderLayout();
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean followingComplementScroll;
private void jbInit() throws Exception
{
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
- this.setLayout(borderLayout7);
+ this.setLayout(new BorderLayout());
// sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
- sequenceHolderPanel.setLayout(borderLayout3);
- seqPanelHolder.setLayout(borderLayout1);
+ sequenceHolderPanel.setLayout(new BorderLayout());
+ seqPanelHolder.setLayout(new BorderLayout());
scalePanelHolder.setBackground(Color.white);
// scalePanelHolder.setPreferredSize(new Dimension(10, 30));
- scalePanelHolder.setLayout(borderLayout6);
- idPanelHolder.setLayout(borderLayout5);
+ scalePanelHolder.setLayout(new BorderLayout());
+ idPanelHolder.setLayout(new BorderLayout());
idSpaceFillerPanel1.setBackground(Color.white);
// idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
- idSpaceFillerPanel1.setLayout(borderLayout11);
+ idSpaceFillerPanel1.setLayout(new BorderLayout());
annotationSpaceFillerHolder.setBackground(Color.white);
// annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
- annotationSpaceFillerHolder.setLayout(borderLayout4);
+ annotationSpaceFillerHolder.setLayout(new BorderLayout());
hscroll.setOrientation(Scrollbar.HORIZONTAL);
- hscrollHolder.setLayout(borderLayout10);
+
+ Panel hscrollHolder = new Panel();
+ hscrollHolder.setLayout(new BorderLayout());
hscrollFillerPanel.setBackground(Color.white);
apvscroll.setOrientation(Scrollbar.VERTICAL);
apvscroll.setVisible(true);
apvscroll.addAdjustmentListener(this);
annotationPanelHolder.setBackground(Color.white);
- annotationPanelHolder.setLayout(borderLayout12);
+ annotationPanelHolder.setLayout(new BorderLayout());
annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
// hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
hscrollHolder.setBackground(Color.white);
error.printStackTrace();
}
+ /**
+ * 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