import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
import jalview.jbgui.GAlignmentPanel;
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;
*/
public void highlightSearchResults(SearchResultsI results)
{
- scrollToPosition(results);
- getSeqPanel().seqCanvas.highlightSearchResults(results);
- }
+ boolean scrolled = scrollToPosition(results, 0, true, false);
- /**
- * Scroll the view to show the position of the highlighted region in results
- * (if any) and redraw the overview
- *
- * @param results
- */
- public boolean scrollToPosition(SearchResultsI results)
- {
- return scrollToPosition(results, 0, true, false);
+ boolean noFastPaint = scrolled && av.getWrapAlignment();
+
+ getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
}
/**
}
/**
- * Scroll the view to show the position of the highlighted region in results
- * (if any)
+ * Scrolls the view (if necessary) to show the position of the first
+ * highlighted region in results (if any). Answers true if the view was
+ * scrolled, or false if no matched region was found, or it is already
+ * visible.
*
* @param results
* @param verticalOffset
* - 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
+ * @return
*/
- public boolean scrollToPosition(SearchResultsI results,
+ protected boolean scrollToPosition(SearchResultsI results,
int verticalOffset, boolean redrawOverview, boolean centre)
{
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?
- // TODO: tons of nullpointerexceptions raised here.
- if (results != null && results.getSize() > 0 && av != null
- && av.getAlignment() != null)
- {
- int seqIndex = av.getAlignment().findIndex(results);
- if (seqIndex == -1)
- {
- return false;
- }
- SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
- int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
- if (r == null)
- {
- return false;
- }
- int start = r[0];
- int end = r[1];
+ if (results == null || results.isEmpty() || av == null
+ || av.getAlignment() == null)
+ {
+ return false;
+ }
+ int seqIndex = av.getAlignment().findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
- /*
- * To centre results, scroll to positions half the visible width
- * left/right of the start/end positions
- */
- if (centre)
- {
- int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
- start = Math.max(start - offset, 0);
- end = end + offset - 1;
- }
- if (start < 0)
- {
- return false;
- }
- if (end == seq.getEnd())
- {
- return false;
- }
- if (av.hasHiddenColumns())
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ 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 = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.findColumnPosition(start);
+ end = hidden.findColumnPosition(end);
+ if (start == end)
{
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- start = hidden.findColumnPosition(start);
- end = hidden.findColumnPosition(end);
- if (start == end)
+ if (!hidden.isVisible(r[0]))
{
- if (!hidden.isVisible(r[0]))
- {
- // don't scroll - position isn't visible
- return false;
- }
+ // don't scroll - position isn't visible
+ return false;
}
}
+ }
- /*
- * allow for offset of target sequence (actually scroll to one above it)
- */
- seqIndex = Math.max(0, seqIndex - verticalOffset);
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+ boolean scrollNeeded = true;
- if (!av.getWrapAlignment())
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = vpRanges.getStartRes()) >= start)
{
- if ((startv = vpRanges.getStartRes()) >= start)
- {
- /*
- * Scroll left to make start of search results visible
- */
- setScrollValues(start, seqIndex);
- }
- else if ((endv = vpRanges.getEndRes()) <= end)
- {
- /*
- * Scroll right to make end of search results visible
- */
- setScrollValues(startv + end - endv, seqIndex);
- }
- else if ((starts = vpRanges.getStartSeq()) > seqIndex)
- {
- /*
- * Scroll up to make start of search results visible
- */
- setScrollValues(vpRanges.getStartRes(), seqIndex);
- }
- else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
- {
- /*
- * Scroll down to make end of search results visible
- */
- setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
- + 1);
- }
/*
- * Else results are already visible - no need to scroll
+ * Scroll left to make start of search results visible
*/
+ setScrollValues(start, seqIndex);
}
- else
+ else if ((endv = vpRanges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
+ }
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
{
- vpRanges.scrollToWrappedVisible(start);
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
+ }
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
}
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ scrollNeeded = false;
+ }
+ else
+ {
+ scrollNeeded = vpRanges.scrollToWrappedVisible(start);
}
paintAlignment(redrawOverview);
- return true;
+
+ return scrollNeeded;
}
/**
annotationSpaceFillerHolder.setVisible(true);
}
- if (wrap)
- {
- int widthInRes = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- vpRanges.setViewportWidth(widthInRes);
- }
- else
- {
- int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
- .getCharWidth()) - 1;
- int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
- .getCharHeight()) - 1;
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+ .getCharHeight()) - 1;
- vpRanges.setViewportWidth(widthInRes);
- vpRanges.setViewportHeight(heightInSeq);
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
}
idSpaceFillerPanel1.setVisible(!wrap);
@Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = vpRanges.getStartRes();
- int oldwidth = vpRanges.getViewportWidth();
- int oldY = vpRanges.getStartSeq();
- int oldheight = vpRanges.getViewportHeight();
-
if (av.getWrapAlignment())
{
- if (evt.getSource() == hscroll)
+ adjustScrollingWrapped(evt);
+ return;
+ }
+
+ if (evt.getSource() == hscroll)
+ {
+ int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+
+ // 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; // no horizontal scroll when wrapped
+ return;
}
- 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))
- {
- return;
- }
- else if (offy > -1)
- {
- vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
- }
- }
- else
+ vpRanges.setViewportStartAndWidth(x, width);
+ }
+ else if (evt.getSource() == vscroll)
+ {
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
+ 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))
{
- // 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);
- }
- });
+ return;
}
+ vpRanges.setViewportStartAndHeight(y, height);
+ }
+ if (!fastPaint)
+ {
repaint();
}
- else
+ }
+
+ /**
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
+ *
+ * @param evt
+ */
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
+ {
+ if (evt.getSource() == hscroll)
{
- // horizontal scroll
- if (evt.getSource() == hscroll)
- {
- int x = hscroll.getValue();
- int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ return; // no horizontal scroll when wrapped
+ }
+ if (evt.getSource() == vscroll)
+ {
+ int newY = vscroll.getValue();
- // 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)
+ /*
+ * 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
+ */
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
{
- 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))
- {
- return;
- }
- vpRanges.setViewportStartAndHeight(y, height);
+ return;
}
- if (!fastPaint)
+ if (newY > -1)
{
- repaint();
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = vpRanges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
}
}
+ else
+ {
+ // 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);
+ }
+ });
+ }
+ repaint();
}
/**
setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
}
- /*
- * Set vertical scroll bar parameters for wrapped panel
- * @param res
- * the residue to scroll to
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
*/
- private void setScrollingForWrappedPanel(int res)
+ private void setScrollingForWrappedPanel(int topLeftColumn)
{
- // get the width of the alignment in residues
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .findColumnPosition(maxwidth) - 1;
- }
-
- // get the width of the canvas in residues
- int canvasWidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (canvasWidth > 0)
- {
- // position we want to scroll to is number of canvasWidth's to get there
- int current = res / canvasWidth;
+ int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
- // 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);
- }
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
}
/**
{
try
{
- int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
- .getAlignment().getWidth(), g, gSize, f, fSize, sy;
+ int sSize = av.getAlignment().getHeight();
+ int alwidth = av.getAlignment().getWidth();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
- out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println(HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
+ "\" border=\"0\" usemap=\"#Map\" >"
+ "<map name=\"Map\">");
- for (s = 0; s < sSize; s++)
+ for (int s = 0; s < sSize; s++)
{
- sy = s * av.getCharHeight() + scaleHeight;
+ int sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
- for (res = 0; res < alwidth; res++)
+ for (int column = 0; column < alwidth; column++)
{
- StringBuilder text = new StringBuilder();
+ StringBuilder text = new StringBuilder(512);
String triplet = null;
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res) + "");
+ .getCharAt(column) + "");
}
else
{
- triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
+ "");
}
continue;
}
- int alIndex = seq.findPosition(res);
- gSize = groups.length;
- for (g = 0; g < gSize; g++)
+ int seqPos = seq.findPosition(column);
+ int gSize = groups.length;
+ for (int g = 0; g < gSize; g++)
{
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\"")
- .append((idWidth + res * av.getCharWidth()))
+ .append((idWidth + column * av.getCharWidth()))
.append(",").append(sy).append(",")
- .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append((idWidth + (column + 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
- && groups[g].getEndRes() > res)
+ if (groups[g].getStartRes() < column
+ && groups[g].getEndRes() > column)
{
text.append("<br><em>").append(groups[g].getName())
.append("</em>");
}
}
- 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 + column * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
+ }
+ if (!Comparison.isGap(seq.getCharAt(column)))
+ {
+ List<SequenceFeature> features = seq.findFeatures(column, column);
+ 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 verticalOffset
* the number of visible sequences to show above the mapped region
*/
- public void scrollToCentre(SearchResultsI sr, int verticalOffset)
+ protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
/*
* To avoid jumpy vertical scrolling (if some sequences are gapped or not
git://source.jalview.org / jalview.git / blobdiff