X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=541c253be796dadb0943a6868953858eeb6e6c72;hb=2fa01dd888f9c0a8e22360fd50015f237184d209;hp=aad07764d1ee3dc246e2ed8c56c62878bf6a666f;hpb=97b26ba418dec7a6e926378205d25470bf098633;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index aad0776..541c253 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -20,9 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.SequenceI; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Font; @@ -31,17 +28,22 @@ import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.RenderingHints; import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; import java.util.List; import javax.swing.JPanel; +import jalview.datamodel.SequenceI; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ -public class IdCanvas extends JPanel +public class IdCanvas extends JPanel implements ViewportListenerI { protected AlignViewport av; @@ -61,10 +63,6 @@ public class IdCanvas extends JPanel List searchResults; - FontMetrics fm; - - AnnotationLabels labels = null; - AnnotationPanel ap; private Font idfont; @@ -80,12 +78,13 @@ public class IdCanvas extends JPanel setLayout(new BorderLayout()); this.av = av; PaintRefresher.Register(this, av.getSequenceSetId()); - } + av.getRanges().addPropertyChangeListener(this); + } /** * DOCUMENT ME! * - * @param gg + * @param g * DOCUMENT ME! * @param hiddenRows * true - check and display hidden row marker if need be @@ -98,7 +97,7 @@ public class IdCanvas extends JPanel * @param ypos * DOCUMENT ME! */ - public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s, + public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s, int i, int starty, int ypos) { int xPos = 0; @@ -107,39 +106,40 @@ public class IdCanvas extends JPanel if ((searchResults != null) && searchResults.contains(s)) { - gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.black); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(s)) { - gg.setColor(Color.lightGray); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.lightGray); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else { - gg.setColor(av.getSequenceColour(s)); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(av.getSequenceColour(s)); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.black); + g.setColor(Color.black); } if (av.isRightAlignIds()) { + FontMetrics fm = g.getFontMetrics(); xPos = panelWidth - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; } - gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); - if (hiddenRows) + if (hiddenRows && av.getShowHiddenMarkers()) { - drawMarker(i, starty, ypos); + drawMarker(g, av, i, starty, ypos); } } @@ -152,7 +152,10 @@ public class IdCanvas extends JPanel */ public void fastPaint(int vertical) { - if (gg == null) + /* + * for now, not attempting fast paint of wrapped ids... + */ + if (gg == null || av.getWrapAlignment()) { repaint(); @@ -193,12 +196,16 @@ public class IdCanvas extends JPanel gg.translate(0, transY); - drawIds(ss, es); + drawIds(gg, av, ss, es, searchResults); gg.translate(0, -transY); fastPaint = true; - repaint(); + + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } /** @@ -210,226 +217,244 @@ public class IdCanvas extends JPanel @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - + if (fastPaint) { fastPaint = false; g.drawImage(image, 0, 0, this); - + return; } - + int oldHeight = imgHeight; - + imgHeight = getHeight(); imgHeight -= (imgHeight % av.getCharHeight()); - + if (imgHeight < 1) { return; } - + if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) { - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); } - + gg = (Graphics2D) image.getGraphics(); - + // Fill in the background gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - - drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq()); - + + drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults); + g.drawImage(image, 0, 0, this); } /** - * DOCUMENT ME! + * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with + * the font and other display settings configured on the viewport. Ids of + * sequences included in the selection are coloured grey, otherwise the + * current id colour for the sequence id is used. * - * @param starty - * DOCUMENT ME! - * @param endy - * DOCUMENT ME! + * @param g + * @param alignViewport + * @param startSeq + * @param endSeq + * @param selection */ - void drawIds(int starty, int endy) + void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq, + final int endSeq, List selection) { - if (av.isSeqNameItalics()) + Font font = alignViewport.getFont(); + if (alignViewport.isSeqNameItalics()) { - setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont() - .getSize())); + setIdfont(new Font(font.getName(), Font.ITALIC, + font.getSize())); } else { - setIdfont(av.getFont()); + setIdfont(font); } - gg.setFont(getIdfont()); - fm = gg.getFontMetrics(); + g.setFont(getIdfont()); + FontMetrics fm = g.getFontMetrics(); - if (av.antiAlias) + if (alignViewport.antiAlias) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } Color currentColor = Color.white; Color currentTextColor = Color.black; - final boolean doHiddenCheck = av.isDisplayReferenceSeq() - || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows(); + boolean hasHiddenRows = alignViewport.hasHiddenRows(); - if (av.getWrapAlignment()) + if (alignViewport.getWrapAlignment()) { - int maxwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getHeight(); + drawIdsWrapped(g, alignViewport, startSeq, getHeight()); + return; + } - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + // Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; - int annotationHeight = 0; + // Now draw the id strings + for (int i = startSeq; i <= endSeq; i++) + { + SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); - if (av.isShowAnnotation()) + if (sequence == null) { - if (ap == null) - { - ap = new AnnotationPanel(av); - } + continue; + } - annotationHeight = ap.adjustPanelHeight(); - if (labels == null) - { - labels = new AnnotationLabels(av); - } + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) + { + g.setFont(getHiddenFont(sequence, alignViewport)); + fm = g.getFontMetrics(); } - int hgap = av.getCharHeight(); - if (av.getScaleAboveWrapped()) + // Selected sequence colours + if (selection != null && selection.contains(sequence)) + { + currentColor = Color.black; + currentTextColor = Color.white; + } + else if ((alignViewport.getSelectionGroup() != null) && alignViewport + .getSelectionGroup().getSequences(null).contains(sequence)) { - hgap += av.getCharHeight(); + currentColor = Color.lightGray; + currentTextColor = Color.black; + } + else + { + currentColor = alignViewport.getSequenceColour(sequence); + currentTextColor = Color.black; } - int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight; + g.setColor(currentColor); - int rowSize = av.getRanges().getEndRes() - - av.getRanges().getStartRes(); + int charHeight = alignViewport.getCharHeight(); + g.fillRect(0, (i - startSeq) * charHeight, + getWidth(), charHeight); - // Draw the rest of the panels - for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getHeight()) - && (row < maxwidth); ypos += cHeight, row += rowSize) - { - for (int i = starty; i < alheight; i++) - { - SequenceI s = av.getAlignment().getSequenceAt(i); - if (doHiddenCheck) - { - setHiddenFont(s); - } - else - { - gg.setFont(getIdfont()); - } - - drawIdString(gg, hiddenRows, s, i, 0, ypos); - } + g.setColor(currentTextColor); - if (labels != null && av.isShowAnnotation()) - { - gg.translate(0, ypos + (alheight * av.getCharHeight())); - labels.drawComponent(gg, getWidth()); - gg.translate(0, -ypos - (alheight * av.getCharHeight())); - } + String string = sequence + .getDisplayId(alignViewport.getShowJVSuffix()); + + if (alignViewport.isRightAlignIds()) + { + xPos = panelWidth - fm.stringWidth(string) - 4; } - } - else - { - // No need to hang on to labels if we're not wrapped - labels = null; - // Now draw the id strings - int panelWidth = getWidth(); - int xPos = 0; + g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); - SequenceI sequence; - // Now draw the id strings - for (int i = starty; i <= endy; i++) + if (hasHiddenRows && av.getShowHiddenMarkers()) { - sequence = av.getAlignment().getSequenceAt(i); - - if (sequence == null) - { - continue; - } + drawMarker(g, alignViewport, i, startSeq, 0); + } + } + } - if (doHiddenCheck) - { - setHiddenFont(sequence); - } + /** + * Draws sequence ids, and annotation labels if annotations are shown, in + * wrapped mode + * + * @param g + * @param alignViewport + * @param startSeq + */ + void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport, + int startSeq, int pageHeight) + { + int alignmentWidth = alignViewport.getAlignment().getWidth(); + final int alheight = alignViewport.getAlignment().getHeight(); - // Selected sequence colours - if ((searchResults != null) && searchResults.contains(sequence)) - { - currentColor = Color.black; - currentTextColor = Color.white; - } - else if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null) - .contains(sequence)) - { - currentColor = Color.lightGray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(sequence); - currentTextColor = Color.black; - } + /* + * assumption: SeqCanvas.calculateWrappedGeometry has been called + */ + SeqCanvas seqCanvas = alignViewport.getAlignPanel() + .getSeqPanel().seqCanvas; - gg.setColor(currentColor); + final int charHeight = alignViewport.getCharHeight(); - gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(), - av.getCharHeight()); + AnnotationLabels labels = null; + if (alignViewport.isShowAnnotation()) + { + labels = new AnnotationLabels(alignViewport); + } - gg.setColor(currentTextColor); + ViewportRanges ranges = alignViewport.getRanges(); - String string = sequence.getDisplayId(av.getShowJVSuffix()); + int rowSize = ranges.getViewportWidth(); - if (av.isRightAlignIds()) + /* + * draw repeating sequence ids until out of sequence data or + * out of visible space, whichever comes first + */ + boolean hasHiddenRows = alignViewport.hasHiddenRows(); + int ypos = seqCanvas.wrappedSpaceAboveAlignment; + int rowStartRes = ranges.getStartRes(); + while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth)) + { + for (int i = startSeq; i < alheight; i++) + { + SequenceI s = alignViewport.getAlignment().getSequenceAt(i); + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) { - xPos = panelWidth - fm.stringWidth(string) - 4; + g.setFont(getHiddenFont(s, alignViewport)); } - - gg.drawString(string, xPos, - (((i - starty) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); - - if (hiddenRows) + else { - drawMarker(i, starty, 0); + g.setFont(getIdfont()); } + drawIdString(g, hasHiddenRows, s, i, 0, ypos); + } + if (labels != null && alignViewport.isShowAnnotation()) + { + g.translate(0, ypos + (alheight * charHeight)); + labels.drawComponent(g, getWidth()); + g.translate(0, -ypos - (alheight * charHeight)); } + ypos += seqCanvas.wrappedRepeatHeightPx; + rowStartRes += rowSize; } } - void drawMarker(int i, int starty, int yoffset) + /** + * Draws a marker (a blue right-pointing triangle) between sequences to + * indicate hidden sequences. + * + * @param g + * @param alignViewport + * @param seqIndex + * @param starty + * @param yoffset + */ + void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset) { - - SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences; + SequenceI[] hseqs = alignViewport.getAlignment() + .getHiddenSequences().hiddenSequences; // Use this method here instead of calling hiddenSeq adjust // 3 times. int hSize = hseqs.length; - int hiddenIndex = i; - int lastIndex = i - 1; - int nextIndex = i + 1; + int hiddenIndex = seqIndex; + int lastIndex = seqIndex - 1; + int nextIndex = seqIndex + 1; for (int j = 0; j < hSize; j++) { @@ -450,48 +475,56 @@ public class IdCanvas extends JPanel } } + /* + * are we below or above the hidden sequences? + */ boolean below = (hiddenIndex > lastIndex + 1); boolean above = (nextIndex > hiddenIndex + 1); - gg.setColor(Color.blue); + g.setColor(Color.blue); + int charHeight = av.getCharHeight(); + + /* + * vertices of the triangle, below or above hidden seqs + */ + int[] xPoints = new int[] + { getWidth() - charHeight, + getWidth() - charHeight, getWidth() }; + int yShift = seqIndex - starty; + if (below) { - gg.fillPolygon( - new int[] { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] { - (i - starty) * av.getCharHeight() + yoffset, - (i - starty) * av.getCharHeight() + yoffset - + av.getCharHeight() / 4, - (i - starty) * av.getCharHeight() + yoffset }, 3); + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset + charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } if (above) { - gg.fillPolygon( - new int[] { getWidth() - av.getCharHeight(), - getWidth() - av.getCharHeight(), getWidth() }, - new int[] { - (i - starty + 1) * av.getCharHeight() + yoffset, - (i - starty + 1) * av.getCharHeight() + yoffset - - av.getCharHeight() / 4, - (i - starty + 1) * av.getCharHeight() + yoffset }, 3); - + yShift++; + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset - charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } } - void setHiddenFont(SequenceI seq) + /** + * Answers the standard sequence id font, or a bold font if the sequence is + * set as reference or a hidden group representative + * + * @param seq + * @param alignViewport + * @return + */ + private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport) { - Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont() - .getSize()); - if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) { - gg.setFont(bold); - } - else - { - gg.setFont(getIdfont()); + return new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); } + return getIdfont(); } /** @@ -515,4 +548,37 @@ public class IdCanvas extends JPanel { this.idfont = idfont; } + + /** + * Respond to viewport range changes (e.g. alignment panel was scrolled). Both + * scrolling and resizing change viewport ranges. Scrolling changes both start + * and end points, but resize only changes end values. Here we only want to + * fastpaint on a scroll, with resize using a normal paint, so scroll events + * are identified as changes to the horizontal or vertical start value. + *

+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll + * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is + * provided, but it generates a change of "startres" which does require an + * update here. + */ + @Override + public void propertyChange(PropertyChangeEvent evt) + { + String propertyName = evt.getPropertyName(); + if (propertyName.equals(ViewportRanges.STARTSEQ) + || (av.getWrapAlignment() + && propertyName.equals(ViewportRanges.STARTRES))) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(((int[]) evt.getNewValue())[1] + - ((int[]) evt.getOldValue())[1]); + } + else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } }