case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ ranges.scrollUp(true);
}
else
{
- alignPanel.setScrollValues(ranges.getStartRes(),
- 2 * ranges.getStartSeq() - ranges.getEndSeq());
+ ranges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ ranges.scrollUp(false);
}
else
{
- alignPanel
- .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
+ ranges.pageDown();
}
break;
return null;
}
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
if (displayTextbox)
*/
package jalview.appletgui;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
UrlProviderI urlProvider = null;
- public IdPanel(AlignViewport av, AlignmentPanel parent)
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
- this.av = av;
+ this.av = viewport;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
// make a list of label,url pairs
HashMap<String, String> urlList = new HashMap<String, String>();
- if (av.applet != null)
+ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
- label = av.applet.getParameter("linkLabel_" + i);
- url = av.applet.getParameter("linkURL_" + i);
+ label = viewport.applet.getParameter("linkLabel_" + i);
+ url = viewport.applet.getParameter("linkURL_" + i);
// only add non-null parameters
if (label != null)
if (!urlList.isEmpty())
{
// set default as first entry in list
- String defaultUrl = av.applet.getParameter("linkLabel_1");
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
UrlProviderFactoryI factory = new AppletUrlProviderFactory(
defaultUrl, urlList);
urlProvider = factory.createUrlProvider();
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- // look for non-pos features
StringBuffer tooltiptext = new StringBuffer();
- if (sequence != null)
+ if (sequence == null)
{
- if (sequence.getDescription() != null)
+ return;
+ }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
+ {
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
{
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
}
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ if (sf.getType() != null)
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
- {
- boolean nl = false;
- if (sf[sl].getFeatureGroup() != null)
- {
- tooltiptext.append(sf[sl].getFeatureGroup());
- nl = true;
- }
- ;
- if (sf[sl].getType() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getType());
- nl = true;
- }
- ;
- if (sf[sl].getDescription() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getDescription());
- nl = true;
- }
- ;
- if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
- {
- tooltiptext.append(" Score = ");
- tooltiptext.append(sf[sl].getScore());
- nl = true;
- }
- ;
- if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
- {
- tooltiptext.append(" (");
- tooltiptext.append(sf[sl].getStatus());
- tooltiptext.append(")");
- nl = true;
- }
- ;
- if (nl)
- {
- tooltiptext.append("\n");
- }
- }
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ if (nl)
+ {
+ tooltiptext.append("\n");
}
}
+
if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
- // build a new links menu based on the current links + any non-positional
- // features
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
List<String> nlinks;
if (urlProvider != null)
{
{
nlinks = new ArrayList<String>();
}
- SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ if (sf.links != null)
{
- if (sf[sl].links != null && sf[sl].links.size() > 0)
+ for (String link : sf.links)
{
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
- {
- nlinks.add(sf[sl].links.elementAt(l));
- }
+ nlinks.add(link);
}
}
}
if (av.getRanges().getStartSeq() > index
|| av.getRanges().getEndSeq() < index)
{
- alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
+ av.getRanges().setStartSeq(index);
}
}
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
- this.up = up;
+ this.up = isUp;
start();
}
running = true;
while (running)
{
- if (alignPanel.scrollUp(up))
+ if (av.getRanges().scrollUp(up))
{
// scroll was ok, so add new sequence to selection
int seq = av.getRanges().getStartSeq();
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+ import jalview.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.List;
import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
endEditing();
if (av.getWrapAlignment())
{
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
while (seqCanvas.cursorY < ranges.getStartSeq())
{
- ap.scrollUp(true);
+ ranges.scrollUp(true);
}
while (seqCanvas.cursorY > ranges.getEndSeq())
{
- ap.scrollUp(false);
+ ranges.scrollUp(false);
}
while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
.getStartRes()))
{
- if (!ap.scrollRight(false))
+ if (!ranges.scrollRight(false))
{
break;
}
while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
.getEndRes()))
{
- if (!ap.scrollRight(true))
+ if (!ranges.scrollRight(true))
{
break;
}
*
* @param sequence
* aligned sequence object
- * @param res
+ * @param column
* alignment column
* @param seq
* index of sequence in alignment
- * @return position of res in sequence
+ * @return position of column in sequence or -1 if at gap
*/
- void setStatusMessage(SequenceI sequence, int res, int seq)
+ void setStatusMessage(SequenceI sequence, int column, int seq)
{
// TODO remove duplication of identical gui method
StringBuilder text = new StringBuilder(32);
/*
* Try to translate the display character to residue name (null for gap).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(res));
+ final String displayChar = String.valueOf(sequence.getCharAt(column));
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
int pos = -1;
if (residue != null)
{
- pos = sequence.findPosition(res);
+ pos = sequence.findPosition(column);
text.append(" (").append(Integer.toString(pos)).append(")");
}
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(sequence,
+ List<SequenceFeature> features = findFeaturesAtRes(sequence,
sequence.findPosition(findRes(evt)));
- if (features != null && features.length > 0)
+ if (!features.isEmpty())
{
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
- {
+ SequenceFeature[] featuresArray = features
+ .toArray(new SequenceFeature[features.size()]);
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[] { sequence }, features, false, ap);
+ new SequenceI[] { sequence }, featuresArray, false, ap);
seqCanvas.highlightSearchResults(null);
}
{
if (av.isFollowHighlight())
{
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
if (ap.scrollToPosition(results, true))
{
ap.alignFrame.repaint();
}
+ ap.setToScrollComplementPanel(true);
}
setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
@Override
public void mouseMoved(MouseEvent evt)
{
- int res = findRes(evt);
+ final int column = findRes(evt);
int seq = findSeq(evt);
- if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+ if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
{
if (tooltip != null)
{
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res > sequence.getLength())
+ if (column > sequence.getLength())
{
if (tooltip != null)
{
return;
}
- int respos = sequence.findPosition(res);
- if (ssm != null)
+ final char ch = sequence.getCharAt(column);
+ int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
+
+ if (ssm != null && respos != -1)
{
- mouseOverSequence(sequence, res, respos);
+ mouseOverSequence(sequence, column, respos);
}
StringBuilder text = new StringBuilder();
.append(" ID: ").append(sequence.getName());
String obj = null;
- final String ch = String.valueOf(sequence.getCharAt(res));
- if (av.getAlignment().isNucleotide())
+ if (respos != -1)
{
- obj = ResidueProperties.nucleotideName.get(ch);
- if (obj != null)
+ if (av.getAlignment().isNucleotide())
{
- text.append(" Nucleotide: ").append(obj);
+ obj = ResidueProperties.nucleotideName.get(ch);
+ if (obj != null)
+ {
+ text.append(" Nucleotide: ").append(obj);
+ }
+ }
+ else
+ {
+ obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
+ .get(String.valueOf(ch));
+ if (obj != null)
+ {
+ text.append(" Residue: ").append(obj);
+ }
}
- }
- else
- {
- obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
- .get(ch);
if (obj != null)
{
- text.append(" Residue: ").append(obj);
+ text.append(" (").append(Integer.toString(respos)).append(")");
}
}
- if (obj != null)
- {
- text.append(" (").append(Integer.toString(respos)).append(")");
- }
-
ap.alignFrame.statusBar.setText(text.toString());
StringBuilder tooltipText = new StringBuilder();
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
}
}
- // use aa to see if the mouse pointer is on a
- List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
-
- int index = 0;
- while (index < allFeatures.size())
+ /*
+ * add feature details to tooltip if over one or more features
+ */
+ if (respos != -1)
{
- SequenceFeature sf = allFeatures.get(index);
-
- tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
-
- if (sf.getDescription() != null)
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(column));
-
- int index = 0;
- while (index < allFeatures.length)
++ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
++ respos);
++ for (SequenceFeature sf : allFeatures)
{
- tooltipText.append(" " + sf.getDescription());
- }
- SequenceFeature sf = allFeatures[index];
-
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
- if (sf.getValue("status") != null)
- {
- String status = sf.getValue("status").toString();
- if (status.length() > 0)
+ if (sf.getDescription() != null)
{
- tooltipText.append(" (" + sf.getValue("status") + ")");
+ tooltipText.append(" " + sf.getDescription());
}
- }
- tooltipText.append("\n");
- index++;
+ if (sf.getValue("status") != null)
+ {
+ String status = sf.getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText.append(" (" + sf.getValue("status") + ")");
+ }
+ }
+ tooltipText.append("\n");
-
- index++;
+ }
}
if (tooltip == null)
}
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
{
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (av.getFeaturesDisplayed() == null
- || !av.getFeaturesDisplayed().isVisible(
- features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && !seqCanvas.fr.checkGroupVisibility(
- features[i].featureGroup, false))
- {
- continue;
- }
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
- }
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
+ return seqCanvas.getFeatureRenderer().findFeaturesAtRes(sequence, res);
}
Tooltip tooltip;
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
sequence.findPosition(res));
Vector<String> links = null;
- if (allFeatures != null)
+ for (int i = 0; i < allFeatures.size(); i++)
{
- for (int i = 0; i < allFeatures.length; i++)
+ SequenceFeature sf = allFeatures.get(i);
+ if (sf.links != null)
{
- if (allFeatures[i].links != null)
+ if (links == null)
{
- if (links == null)
- {
- links = new Vector<String>();
- }
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
+ links = new Vector<String>();
}
+ links.addAll(sf.links);
}
}
APopupMenu popup = new APopupMenu(ap, null, links);
if (mouseDragging && evt.getY() < 0
&& av.getRanges().getStartSeq() > 0)
{
- running = ap.scrollUp(true);
+ running = av.getRanges().scrollUp(true);
}
if (mouseDragging && evt.getY() >= getSize().height
&& av.getAlignment().getHeight() > av.getRanges()
.getEndSeq())
{
- running = ap.scrollUp(false);
+ running = av.getRanges().scrollUp(false);
}
if (mouseDragging && evt.getX() < 0)
{
- running = ap.scrollRight(false);
+ running = av.getRanges().scrollRight(false);
}
else if (mouseDragging && evt.getX() >= getSize().width)
{
- running = ap.scrollRight(true);
+ running = av.getRanges().scrollRight(true);
}
}
*/
package jalview.datamodel;
+import jalview.datamodel.features.SequenceFeaturesI;
+
import java.util.List;
import java.util.Vector;
public String getDescription();
/**
- * Return the alignment column for a sequence position
+ * Return the alignment column (from 1..) for a sequence position
*
* @param pos
* lying from start to end
public int findIndex(int pos);
/**
- * Returns the sequence position for an alignment position
+ * Returns the sequence position for an alignment position.
*
* @param i
* column index in alignment (from 0..<length)
*
- * @return residue number for residue (left of and) nearest ith column
+ * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+ * ith column
*/
public int findPosition(int i);
/**
+ * Returns the range of sequence positions included in the given alignment
+ * position range. If no positions are included (the range is entirely gaps),
+ * then returns null.
+ *
+ * <pre>
+ * Example:
+ * >Seq/8-13
+ * ABC--DE-F
+ * findPositions(1, 4) returns Range(9, 9) // B only
+ * findPositions(3, 4) returns null // all gaps
+ * findPositions(2, 6) returns Range(10, 12) // CDE
+ * findPositions(3, 7) returns Range(11,12) // DE
+ * </pre>
+ *
+ * @param fromCol
+ * first aligned column position (base 0, inclusive)
+ * @param toCol
+ * last aligned column position (base 0, inclusive)
+ *
+ * @return
+ */
+ public Range findPositions(int fromCol, int toCol);
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
public void insertCharAt(int position, int count, char ch);
/**
- * Gets array holding sequence features associated with this sequence. The
- * array may be held by the sequence's dataset sequence if that is defined.
+ * Answers a list of all sequence features associated with this sequence. The
+ * list may be held by the sequence's dataset sequence if that is defined.
*
* @return hard reference to array
*/
- public SequenceFeature[] getSequenceFeatures();
+ public List<SequenceFeature> getSequenceFeatures();
+
+ /**
+ * Answers the object holding features for the sequence
+ *
+ * @return
+ */
+ SequenceFeaturesI getFeatures();
/**
- * Replaces the array of sequence features associated with this sequence with
- * a new array reference. If this sequence has a dataset sequence, then this
- * method will update the dataset sequence's feature array
+ * Replaces the sequence features associated with this sequence with the given
+ * features. If this sequence has a dataset sequence, then this method will
+ * update the dataset sequence's features instead.
*
* @param features
- * New array of sequence features
*/
- public void setSequenceFeatures(SequenceFeature[] features);
+ public void setSequenceFeatures(List<SequenceFeature> features);
/**
* DOCUMENT ME!
/**
* Adds the given sequence feature and returns true, or returns false if it is
- * already present on the sequence
+ * already present on the sequence, or if the feature type is null.
*
* @param sf
* @return
* list
*/
public List<DBRefEntry> getPrimaryDBRefs();
+
+ /**
+ * Returns a (possibly empty) list of sequence features that overlap the range
+ * from-to (inclusive), optionally restricted to one or more specified feature
+ * types
+ *
+ * @param from
+ * @param to
+ * @param types
+ * @return
+ */
+ List<SequenceFeature> findFeatures(int from, int to, String... types);
}
import jalview.math.AlignmentDimension;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.Platform;
+ import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Insets;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
+ import java.awt.event.ComponentAdapter;
+ import java.awt.event.ComponentEvent;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
* @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel
+ AdjustmentListener, Printable, AlignmentViewPanel,
+ ViewportListenerI
{
public AlignViewport av;
/*
* Flag set while scrolling to follow complementary cDNA/protein scroll. When
- * true, suppresses invoking the same method recursively.
+ * false, suppresses invoking the same method recursively.
*/
- private boolean dontScrollComplement;
+ private boolean scrollComplementaryPanel = true;
private PropertyChangeListener propertyChangeListener;
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
final AlignmentPanel ap = this;
propertyChangeListener = new PropertyChangeListener()
{
}
};
av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
fontChanged();
adjustAnnotationHeight();
updateLayout();
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
if (this.alignFrame.getSplitViewContainer() != null)
{
((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
}
int start = r[0];
int end = r[1];
- // DEBUG
- // System.err.println(this.av.viewName + " Seq : " + seqIndex
- // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
*/
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 = vpRanges.getStartRes()) >= start)
/*
* Scroll left to make start of search results visible
*/
- // setScrollValues(start - 1, seqIndex); // plus one residue
setScrollValues(start, seqIndex);
}
else if ((endv = vpRanges.getEndRes()) <= end)
/*
* Scroll right to make end of search results visible
*/
- // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
setScrollValues(startv + end - endv, seqIndex);
}
else if ((starts = vpRanges.getStartSeq()) > seqIndex)
}
else
{
- scrollToWrappedVisible(start);
+ vpRanges.scrollToWrappedVisible(start);
}
}
- if (redrawOverview && overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
+
paintAlignment(redrawOverview);
return true;
}
- void scrollToWrappedVisible(int res)
- {
- int cwidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (res < vpRanges.getStartRes()
- || res >= (vpRanges.getStartRes() + cwidth))
- {
- vscroll.setValue((res / cwidth));
- vpRanges.setStartRes(vscroll.getValue() * cwidth);
- }
-
- }
-
/**
* DOCUMENT ME!
*
annotationSpaceFillerHolder.setVisible(true);
}
- idSpaceFillerPanel1.setVisible(!wrap);
-
- repaint();
- }
-
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if (up)
+ if (wrap)
{
- if (vscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
}
else
{
- if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
- {
- return false;
- }
+ int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+ .getCharHeight()) - 1;
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
}
- fastPaint = true;
+ idSpaceFillerPanel1.setVisible(!wrap);
- return true;
+ repaint();
}
- /**
- * DOCUMENT ME!
- *
- * @param right
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean scrollRight(boolean right)
- {
- if (!right)
- {
- if (hscroll.getValue() < 1)
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
- {
- return false;
- }
-
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
-
- fastPaint = true;
-
- return true;
- }
/**
* Adjust row/column scrollers to show a visible position in the alignment.
* visible row to scroll to
*
*/
- public void setScrollValues(int x, int y)
+ public void setScrollValues(int xpos, int ypos)
{
+ int x = xpos;
+ int y = ypos;
+
if (av == null || av.getAlignment() == null)
{
return;
}
- int width = av.getAlignment().getWidth();
- int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
+ if (av.getWrapAlignment())
{
- // reset the width to exclude hidden columns
- width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
+ setScrollingForWrappedPanel(x);
}
+ else
+ {
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
- hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
- vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+ if (av.hasHiddenColumns())
+ {
+ // reset the width to exclude hidden columns
+ width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
+ }
- if (hextent > width)
- {
- hextent = width;
- }
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
- if (vextent > height)
- {
- vextent = height;
- }
+ if (hextent > width)
+ {
+ hextent = width;
+ }
- if ((hextent + x) > width)
- {
- x = width - hextent;
- }
+ if (vextent > height)
+ {
+ vextent = height;
+ }
- if ((vextent + y) > height)
- {
- y = height - vextent;
- }
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
- if (y < 0)
- {
- y = 0;
- }
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
- if (x < 0)
- {
- x = 0;
- }
+ if (y < 0)
+ {
+ y = 0;
+ }
- // update endRes after x has (possibly) been adjusted
- vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
+ if (x < 0)
+ {
+ 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);
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
}
/**
- * DOCUMENT ME!
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
*
* @param evt
- * DOCUMENT ME!
+ * adjustment event encoding whether hscroll or vscroll changed
*/
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.getViewportWidth();
int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- vpRanges.setStartRes(x);
- vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
- }
-
- if (evt.getSource() == vscroll)
+ if (av.getWrapAlignment())
{
- int offy = vscroll.getValue();
-
- if (av.getWrapAlignment())
+ if (evt.getSource() == hscroll)
{
- if (offy > -1)
+ return; // no horizontal scroll when wrapped
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+ int rowSize = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((offy * rowSize == oldX) && (oldwidth == rowSize))
{
- int rowSize = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- vpRanges.setStartRes(offy * rowSize);
- vpRanges.setEndRes((offy + 1) * rowSize);
+ return;
}
- else
+ else if (offy > -1)
{
- // This is only called if file loaded is a jar file that
- // was wrapped when saved and user has wrap alignment true
- // as preference setting
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- setScrollValues(vpRanges.getStartRes(),
- vpRanges.getStartSeq());
- }
- });
+ vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
}
}
else
{
- vpRanges.setStartSeq(offy);
- vpRanges.setEndSeq(offy
- + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
- - 1);
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log
+ .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ vpRanges.setStartRes(0);
+ vpRanges.setStartSeq(0);
+ }
+ });
}
- }
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- int scrollX = vpRanges.getStartRes() - oldX;
- int scrollY = vpRanges.getStartSeq() - oldY;
-
- if (av.getWrapAlignment() || !fastPaint)
- {
repaint();
}
else
{
- // Make sure we're not trying to draw a panel
- // larger than the visible window
- if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+ // horizontal scroll
+ if (evt.getSource() == hscroll)
{
- scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
- }
- else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
- {
- scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
- }
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
- if (scrollX != 0 || scrollY != 0)
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
{
- getIdPanel().getIdCanvas().fastPaint(scrollY);
- getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
- getScalePanel().repaint();
-
- if (av.isShowAnnotation() && scrollX != 0)
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((y == oldY) && (height == oldheight))
{
- getAnnotationPanel().fastPaint(scrollX);
+ return;
}
+ vpRanges.setViewportStartAndHeight(y, height);
+ }
+ if (!fastPaint)
+ {
+ repaint();
}
- }
- /*
- * If there is one, scroll the (Protein/cDNA) complementary alignment to
- * match, unless we are ourselves doing that.
- */
- if (isDontScrollComplement())
- {
- setDontScrollComplement(false);
- }
- else
- {
- av.scrollComplementaryAlignment();
}
}
validate();
/*
- * set scroll bar positions; first suppress this being 'followed' in any
- * complementary split pane
+ * set scroll bar positions
*/
- setDontScrollComplement(true);
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ }
- if (av.getWrapAlignment())
+ /*
+ * Set vertical scroll bar parameters for wrapped panel
+ * @param res
+ * the residue to scroll to
+ */
+ private void setScrollingForWrappedPanel(int res)
+ {
+ // get the width of the alignment in residues
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
maxwidth = av.getAlignment().getHiddenColumns()
.findColumnPosition(maxwidth) - 1;
- }
-
- int canvasWidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (canvasWidth > 0)
- {
- int max = maxwidth
- / getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas
- .getWidth()) + 1;
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
}
- else
+
+ // get the width of the canvas in residues
+ int canvasWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ if (canvasWidth > 0)
{
- setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ // position we want to scroll to is number of canvasWidth's to get there
+ int current = res / canvasWidth;
+
+ // max scroll position: add one because extent is 1 and scrollbar value
+ // can only be set to at most max - extent
+ int max = maxwidth / canvasWidth + 1;
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(current, 1, 0, max);
}
}
sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
- StringBuilder text = new StringBuilder();
+ StringBuilder text = new StringBuilder(512);
String triplet = null;
if (av.getAlignment().isNucleotide())
{
continue;
}
- int alIndex = seq.findPosition(res);
+ int seqPos = seq.findPosition(res);
gSize = groups.length;
for (g = 0; g < gSize; g++)
{
.append((idWidth + (res + 1) * av.getCharWidth()))
.append(",").append((av.getCharHeight() + sy))
.append("\"").append(" onMouseOver=\"toolTip('")
- .append(alIndex).append(" ").append(triplet);
+ .append(seqPos).append(" ").append(triplet);
}
if (groups[g].getStartRes() < res
}
}
- if (features != null)
+ if (text.length() < 1)
{
- if (text.length() < 1)
- {
- text.append("<area shape=\"rect\" coords=\"")
- .append((idWidth + res * av.getCharWidth()))
- .append(",").append(sy).append(",")
- .append((idWidth + (res + 1) * av.getCharWidth()))
- .append(",").append((av.getCharHeight() + sy))
- .append("\"").append(" onMouseOver=\"toolTip('")
- .append(alIndex).append(" ").append(triplet);
- }
- fSize = features.length;
- for (f = 0; f < fSize; f++)
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
+ }
+ if (!Comparison.isGap(seq.getCharAt(res)))
+ {
+ List<SequenceFeature> features = seq.getFeatures()
+ .findFeatures(seqPos, seqPos);
+ for (SequenceFeature sf : features)
{
-
- if ((features[f].getBegin() <= seq.findPosition(res))
- && (features[f].getEnd() >= seq.findPosition(res)))
+ if (sf.isContactFeature())
{
- if (features[f].isContactFeature())
- {
- if (features[f].getBegin() == seq.findPosition(res)
- || features[f].getEnd() == seq
- .findPosition(res))
- {
- text.append("<br>").append(features[f].getType())
- .append(" ").append(features[f].getBegin())
- .append(":").append(features[f].getEnd());
- }
- }
- else
+ text.append("<br>").append(sf.getType()).append(" ")
+ .append(sf.getBegin()).append(":")
+ .append(sf.getEnd());
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(sf.getType());
+ String description = sf.getDescription();
+ if (description != null
+ && !sf.getType().equals(description))
{
- text.append("<br>");
- text.append(features[f].getType());
- if (features[f].getDescription() != null
- && !features[f].getType().equals(
- features[f].getDescription()))
- {
- text.append(" ").append(features[f].getDescription());
- }
-
- if (features[f].getValue("status") != null)
- {
- text.append(" (").append(features[f].getValue("status"))
- .append(")");
- }
+ description = description.replace("\"", """);
+ text.append(" ").append(description);
}
}
-
+ String status = sf.getStatus();
+ if (status != null && !"".equals(status))
+ {
+ text.append(" (").append(status).append(")");
+ }
+ }
+ if (text.length() > 1)
+ {
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
+ out.println(text.toString());
}
- }
- if (text.length() > 1)
- {
- text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
- out.println(text.toString());
}
}
}
*
* @param b
*/
- protected void setDontScrollComplement(boolean b)
+ protected void setToScrollComplementPanel(boolean b)
{
- this.dontScrollComplement = b;
+ this.scrollComplementaryPanel = b;
}
- protected boolean isDontScrollComplement()
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
{
- return this.dontScrollComplement;
+ return this.scrollComplementaryPanel;
}
/**
}
}
+ @Override
+ /**
+ * Property change event fired when a change is made to the viewport ranges
+ * object associated with this alignment panel's viewport
+ */
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // update this panel's scroll values based on the new viewport ranges values
+ int x = vpRanges.getStartRes();
+ int y = vpRanges.getStartSeq();
+ setScrollValues(x, y);
+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment();
+ setToScrollComplementPanel(true);
+ }
+ }
+
/**
* Set the reference to the PCA/Tree chooser dialog for this panel. This
* reference should be nulled when the dialog is closed.
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
else
{
- alignPanel.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else
{
- alignPanel.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
}
{
int seq2 = alignPanel.getSeqPanel().findSeq(e);
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
- // build a new links menu based on the current links + any non-positional
- // features
+
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
- SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
- if (sfs != null)
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
- for (SequenceFeature sf : sfs)
+ if (sf.links != null)
{
- if (sf.begin == sf.end && sf.begin == 0)
+ for (String link : sf.links)
{
- if (sf.links != null && sf.links.size() > 0)
- {
- for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
- {
- nlinks.add(sf.links.elementAt(l));
- }
- }
+ nlinks.add(link);
}
}
}
if ((av.getRanges().getStartSeq() > index)
|| (av.getRanges().getEndSeq() < index))
{
- alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
+ av.getRanges().setStartSeq(index);
}
}
while (running)
{
- if (alignPanel.scrollUp(up))
+ if (av.getRanges().scrollUp(up))
{
// scroll was ok, so add new sequence to selection
int seq = av.getRanges().getStartSeq();
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
// TODO: omit sequence features from each alignment view's XML dump if we
// are storing dataset
- if (jds.getSequenceFeatures() != null)
+ List<jalview.datamodel.SequenceFeature> sfs = jds
+ .getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
- int index = 0;
- while (index < sf.length)
- {
- Features features = new Features();
+ Features features = new Features();
- features.setBegin(sf[index].getBegin());
- features.setEnd(sf[index].getEnd());
- features.setDescription(sf[index].getDescription());
- features.setType(sf[index].getType());
- features.setFeatureGroup(sf[index].getFeatureGroup());
- features.setScore(sf[index].getScore());
- if (sf[index].links != null)
+ features.setBegin(sf.getBegin());
+ features.setEnd(sf.getEnd());
+ features.setDescription(sf.getDescription());
+ features.setType(sf.getType());
+ features.setFeatureGroup(sf.getFeatureGroup());
+ features.setScore(sf.getScore());
+ if (sf.links != null)
+ {
+ for (int l = 0; l < sf.links.size(); l++)
{
- for (int l = 0; l < sf[index].links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_" + l);
- keyValue.setValue(sf[index].links.elementAt(l).toString());
- features.addOtherData(keyValue);
- }
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf.links.elementAt(l).toString());
+ features.addOtherData(keyValue);
}
- if (sf[index].otherDetails != null)
+ }
+ if (sf.otherDetails != null)
+ {
+ String key;
+ Iterator<String> keys = sf.otherDetails.keySet().iterator();
+ while (keys.hasNext())
{
- String key;
- Iterator<String> keys = sf[index].otherDetails.keySet()
- .iterator();
- while (keys.hasNext())
- {
- key = keys.next();
- OtherData keyValue = new OtherData();
- keyValue.setKey(key);
- keyValue.setValue(sf[index].otherDetails.get(key).toString());
- features.addOtherData(keyValue);
- }
+ key = keys.next();
+ OtherData keyValue = new OtherData();
+ keyValue.setKey(key);
+ keyValue.setValue(sf.otherDetails.get(key).toString());
+ features.addOtherData(keyValue);
}
-
- jseq.addFeatures(features);
- index++;
}
+
+ jseq.addFeatures(features);
}
if (jdatasq.getAllPDBEntries() != null)
Features[] features = jseqs[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
- features[f].getEnd(), features[f].getFeatureGroup());
-
- sf.setScore(features[f].getScore());
+ SequenceFeature sf = new SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getScore(),
+ features[f].getFeatureGroup());
+ sf.setStatus(features[f].getStatus());
for (int od = 0; od < features[f].getOtherDataCount(); od++)
{
OtherData keyValue = features[f].getOtherData(od);
af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
.isShowUnconserved() : false);
af.viewport.getRanges().setStartRes(view.getStartRes());
- af.viewport.getRanges().setStartSeq(view.getStartSeq());
+ // startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
// apply colourschemes
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
Features[] features = JSEQ[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
+ SequenceFeature sf = new SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getBegin(),
features[f].getEnd(), null);
-
+ sf.setStatus(features[f].getStatus());
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
}
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
af.viewport.getRanges().setStartRes(view.getStartRes());
- af.viewport.getRanges().setStartSeq(view.getStartSeq());
+ // startSeq set in af.alignPanel.updateLayout below
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setColourText(view.getShowColourText());
/** DOCUMENT ME!! */
public AlignmentPanel ap;
+ /*
+ * last column position for mouseMoved event
+ */
+ private int lastMouseColumn;
+
+ /*
+ * last sequence offset for mouseMoved event
+ */
+ private int lastMouseSeq;
+
protected int lastres;
protected int startseq;
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
+
+ lastMouseColumn = -1;
+ lastMouseSeq = -1;
}
int startWrapBlock = -1;
endEditing();
if (av.getWrapAlignment())
{
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
- while (seqCanvas.cursorY < av.getRanges().getStartSeq())
- {
- ap.scrollUp(true);
- }
- while (seqCanvas.cursorY > av.getRanges().getEndSeq())
- {
- ap.scrollUp(false);
- }
- if (!av.getWrapAlignment())
- {
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
- .getRanges().getStartRes()))
- {
- if (!ap.scrollRight(false))
- {
- break;
- }
- }
- while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
- .getRanges().getEndRes()))
- {
- if (!ap.scrollRight(true))
- {
- break;
- }
- }
- }
+ av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
+ av);
}
setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
if (av.isFollowHighlight())
{
- /*
- * if scrollToPosition requires a scroll adjustment, this flag prevents
- * another scroll event being propagated back to the originator
- *
- * @see AlignmentPanel#adjustmentValueChanged
- */
- ap.setDontScrollComplement(true);
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
if (ap.scrollToPosition(results, false))
{
seqCanvas.revalidate();
}
+ ap.setToScrollComplementPanel(true);
}
setStatusMessage(results);
seqCanvas.highlightSearchResults(results);
{
return;
}
+ if (column == lastMouseColumn && seq == lastMouseSeq)
+ {
+ /*
+ * just a pixel move without change of residue
+ */
+ return;
+ }
+ lastMouseColumn = column;
+ lastMouseSeq = seq;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
}
}
- if (av.isShowSequenceFeatures())
+ if (av.isShowSequenceFeatures() && pos != -1)
{
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(), pos);
}
else
{
- if (lastTooltip == null
- || !lastTooltip.equals(tooltipText.toString()))
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
{
String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
- tooltipText.toString());
- // String formatedTooltipText = tooltipText.toString();
+ textString);
setToolTipText(formatedTooltipText);
- lastTooltip = tooltipText.toString();
+ lastTooltip = textString;
}
-
}
-
}
private Point lastp = null;
/**
* Sets the status message in alignment panel, showing the sequence number
* (index) and id, residue and residue position for the given sequence and
- * column position. Returns the calculated residue position in the sequence.
+ * column position. Returns the calculated residue position in the sequence,
+ * or -1 for a gapped column position.
*
* @param sequence
* aligned sequence object
* alignment column
* @param seq
* index of sequence in alignment
- * @return position of res in sequence
+ * @return position of column in sequence or -1 if at a gap
*/
int setStatusMessage(SequenceI sequence, final int column, int seq)
{
{
if (e.isShiftDown())
{
- ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
else
{
- ap.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
- ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else
{
- ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
// TODO Update tooltip for new position.
if (mouseDragging && (evt.getY() < 0)
&& (av.getRanges().getStartSeq() > 0))
{
- running = ap.scrollUp(true);
+ running = av.getRanges().scrollUp(true);
}
if (mouseDragging && (evt.getY() >= getHeight())
&& (av.getAlignment().getHeight() > av.getRanges()
.getEndSeq()))
{
- running = ap.scrollUp(false);
+ running = av.getRanges().scrollUp(false);
}
if (mouseDragging && (evt.getX() < 0))
{
- running = ap.scrollRight(false);
+ running = av.getRanges().scrollRight(false);
}
else if (mouseDragging && (evt.getX() >= getWidth()))
{
- running = ap.scrollRight(true);
+ running = av.getRanges().scrollRight(true);
}
}
git://source.jalview.org / jalview.git / commitdiff