X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=e8cc68bc69763f400f40cf6b3c5e7ffa43b5a3fc;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=056a602768b5debbb85d18bc5de50ad6c7af523e;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 056a602..e8cc68b 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -62,7 +62,6 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.ListIterator; import javax.swing.JPanel; import javax.swing.SwingUtilities; @@ -85,6 +84,16 @@ public class SeqPanel extends JPanel /** 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; @@ -171,6 +180,9 @@ public class SeqPanel extends JPanel ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } + + lastMouseColumn = -1; + lastMouseSeq = -1; } int startWrapBlock = -1; @@ -204,7 +216,7 @@ public class SeqPanel extends JPanel int y = evt.getY(); y -= hgap; - x = Math.max(0, x - seqCanvas.LABEL_WEST); + x = Math.max(0, x - seqCanvas.labelWidthWest); int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -669,6 +681,8 @@ public class SeqPanel extends JPanel } lastSearchResults = results; + boolean wasScrolled = false; + if (av.isFollowHighlight()) { // don't allow highlight of protein/cDNA to also scroll a complementary @@ -676,14 +690,19 @@ public class SeqPanel extends JPanel // 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)) + wasScrolled = ap.scrollToPosition(results, false); + if (wasScrolled) { seqCanvas.revalidate(); } ap.setToScrollComplementPanel(true); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); + } } @Override @@ -719,8 +738,18 @@ public class SeqPanel extends JPanel int seq = findSeq(evt); if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { + lastMouseSeq = -1; 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); @@ -771,11 +800,7 @@ public class SeqPanel extends JPanel if (av.isShowSequenceFeatures()) { List features = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), pos); - if (isGapped) - { - removeAdjacentFeatures(features, column + 1, sequence); - } + .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -786,45 +811,13 @@ public class SeqPanel extends JPanel } else { - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) - { - String formatedTooltipText = JvSwingUtils.wrapTooltip(true, - tooltipText.toString()); - // String formatedTooltipText = tooltipText.toString(); - setToolTipText(formatedTooltipText); - lastTooltip = tooltipText.toString(); - } - - } - - } - - /** - * Removes from the list of features any that start after, or end before, the - * given column position. This allows us to retain only those features - * adjacent to a gapped position that straddle the position. Contact features - * that 'straddle' the position are also removed, since they are not 'at' the - * position. - * - * @param features - * @param column - * alignment column (1..) - * @param sequence - */ - protected void removeAdjacentFeatures(List features, - final int column, SequenceI sequence) - { - // TODO should this be an AlignViewController method (and reused by applet)? - ListIterator it = features.listIterator(); - while (it.hasNext()) - { - SequenceFeature sf = it.next(); - if (sf.isContactFeature() - || sequence.findIndex(sf.getBegin()) > column - || sequence.findIndex(sf.getEnd()) < column) + String textString = tooltipText.toString(); + if (lastTooltip == null || !lastTooltip.equals(textString)) { - it.remove(); + String formattedTooltipText = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(formattedTooltipText); + lastTooltip = textString; } } } @@ -883,19 +876,48 @@ public class SeqPanel extends JPanel * aligned sequence object * @param column * alignment column - * @param seq + * @param seqIndex * index of sequence in alignment * @return sequence position of residue at column, or adjacent residue if at a * gap */ - int setStatusMessage(SequenceI sequence, final int column, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seqIndex) + { + char sequenceChar = sequence.getCharAt(column); + int pos = sequence.findPosition(column); + setStatusMessage(sequence, seqIndex, sequenceChar, pos); + + return pos; + } + + /** + * Builds the status message for the current cursor location and writes it to + * the status bar, for example + * + * 
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   *
+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); @@ -904,13 +926,12 @@ public class SeqPanel extends JPanel /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(column)); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); - int pos = sequence.findPosition(column); + boolean isGapped = Comparison.isGap(sequenceChar); if (!isGapped) { boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); if (nucleotide) { residue = ResidueProperties.nucleotideName.get(displayChar); @@ -924,11 +945,9 @@ public class SeqPanel extends JPanel text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") .append(": ").append(residue == null ? displayChar : residue); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - - return pos; } /** @@ -956,12 +975,9 @@ public class SeqPanel extends JPanel if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } @@ -1258,7 +1274,7 @@ public class SeqPanel extends JPanel // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--) + for (; fixedRight > lastres; fixedRight--) { blank = true; @@ -1568,19 +1584,13 @@ public class SeqPanel extends JPanel } int column = findColumn(evt); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); /* * find features at the position (if not gapped), or straddling * the position (if at a gap) */ List features = seqCanvas.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(column)); - if (isGapped) - { - removeAdjacentFeatures(features, column, sequence); - } + .findFeaturesAtColumn(sequence, column + 1); if (!features.isEmpty()) { @@ -1588,9 +1598,9 @@ public class SeqPanel extends JPanel * highlight the first feature at the position on the alignment */ SearchResultsI highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), - features.get(0).getEnd()); - seqCanvas.highlightSearchResults(highlight); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); + seqCanvas.highlightSearchResults(highlight, false); /* * open the Amend Features dialog; clear highlighting afterwards, @@ -1599,7 +1609,8 @@ public class SeqPanel extends JPanel List seqs = Collections.singletonList(sequence); seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, ap); - seqCanvas.highlightSearchResults(null); + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features } } } @@ -1758,12 +1769,11 @@ public class SeqPanel extends JPanel */ void showPopupMenu(MouseEvent evt) { - final int res = findColumn(evt); + final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); + .findFeaturesAtColumn(sequence, column + 1); List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) {