X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=541c253be796dadb0943a6868953858eeb6e6c72;hb=2fa01dd888f9c0a8e22360fd50015f237184d209;hp=882ed7ae2aa060d5451a8c9674d0d93965008f03;hpb=5150ffd5baa1f58bb6b4059616bc6b9050326553;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 882ed7a..541c253 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,201 +1,584 @@ -package jalview.gui; - -import java.awt.*; -import java.awt.Graphics2D.*; -import java.awt.image.*; -import javax.swing.*; -import jalview.datamodel.*; -import jalview.analysis.*; -public class IdCanvas extends JPanel -{ - protected AlignViewport av; - - protected boolean showScores = true; - - protected int maxIdLength = -1; - protected String maxIdStr = null; - BufferedImage image; - Graphics2D gg; - int imgHeight=0; - boolean fastPaint = false; - - java.util.Vector searchResults; - - public IdCanvas(AlignViewport av) - { - setLayout(new BorderLayout()); - this.av = av; - PaintRefresher.Register(this); - } - - public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) { - int charHeight = av.getCharHeight(); - - if(searchResults!=null && searchResults.contains(s)) - { - gg.setColor(Color.black); - gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight); - gg.setColor(Color.white); - } - else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) { - gg.setColor(Color.lightGray); - gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight); - gg.setColor(Color.white); - } else { - gg.setColor(s.getColor()); - gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight); - gg.setColor(Color.black); - } - - String string = s.getName(); - if(av.getShowFullId()) - string = s.getDisplayId(); - - gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5)); - - } - - public void fastPaint(int vertical) - { - if(gg==null) - { repaint(); return;} - - gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight ); - - int ss=av.startSeq, es=av.endSeq, transY = 0; - if (vertical > 0) // scroll down - { - ss = es - vertical; - if(ss av.endSeq) - es = av.endSeq; - } - - - - gg.translate(0, transY); - - drawIds(ss, es); - - gg.translate( 0, -transY ); - - - fastPaint = true; - repaint(); - } - - public void paintComponent(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - - if (fastPaint) - { - fastPaint = false; - g.drawImage(image, 0, 0, this); - return; - } - - imgHeight = getHeight(); - imgHeight -= imgHeight % av.charHeight; - 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); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - gg.setFont(italic); - - drawIds( av.getStartSeq(), av.endSeq); - - g.drawImage(image, 0, 0, this); - } - - void drawIds(int starty, int endy) - { - Color currentColor = Color.white; - Color currentTextColor = Color.black; - - if (av.getWrapAlignment()) - { - - int rowSize = av.getEndRes() - av.getStartRes(); - // Draw the rest of the panels - - for(int ypos=2*av.charHeight, row=av.startRes; - ypos <= getHeight() && row. + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +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 implements ViewportListenerI +{ + protected AlignViewport av; + + protected boolean showScores = true; + + protected int maxIdLength = -1; + + protected String maxIdStr = null; + + BufferedImage image; + + Graphics2D gg; + + int imgHeight = 0; + + boolean fastPaint = false; + + List searchResults; + + AnnotationPanel ap; + + private Font idfont; + + /** + * Creates a new IdCanvas object. + * + * @param av + * DOCUMENT ME! + */ + public IdCanvas(AlignViewport av) + { + setLayout(new BorderLayout()); + this.av = av; + PaintRefresher.Register(this, av.getSequenceSetId()); + av.getRanges().addPropertyChangeListener(this); + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param hiddenRows + * true - check and display hidden row marker if need be + * @param s + * DOCUMENT ME! + * @param i + * DOCUMENT ME! + * @param starty + * DOCUMENT ME! + * @param ypos + * DOCUMENT ME! + */ + public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s, + int i, int starty, int ypos) + { + int xPos = 0; + int panelWidth = getWidth(); + int charHeight = av.getCharHeight(); + + if ((searchResults != null) && searchResults.contains(s)) + { + g.setColor(Color.black); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + g.setColor(Color.white); + } + else if ((av.getSelectionGroup() != null) + && av.getSelectionGroup().getSequences(null).contains(s)) + { + g.setColor(Color.lightGray); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + g.setColor(Color.white); + } + else + { + g.setColor(av.getSequenceColour(s)); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + g.setColor(Color.black); + } + + if (av.isRightAlignIds()) + { + FontMetrics fm = g.getFontMetrics(); + xPos = panelWidth + - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; + } + + g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); + + if (hiddenRows && av.getShowHiddenMarkers()) + { + drawMarker(g, av, i, starty, ypos); + } + + } + + /** + * DOCUMENT ME! + * + * @param vertical + * DOCUMENT ME! + */ + public void fastPaint(int vertical) + { + /* + * for now, not attempting fast paint of wrapped ids... + */ + if (gg == null || av.getWrapAlignment()) + { + repaint(); + + return; + } + + ViewportRanges ranges = av.getRanges(); + + gg.copyArea(0, 0, getWidth(), imgHeight, 0, + -vertical * av.getCharHeight()); + + int ss = ranges.getStartSeq(); + int es = ranges.getEndSeq(); + int transY = 0; + + if (vertical > 0) // scroll down + { + ss = es - vertical; + + if (ss < ranges.getStartSeq()) + { // ie scrolling too fast, more than a page at a time + ss = ranges.getStartSeq(); + } + else + { + transY = imgHeight - ((vertical + 1) * av.getCharHeight()); + } + } + else if (vertical < 0) // scroll up + { + es = ss - vertical; + + if (es > ranges.getEndSeq()) + { + es = ranges.getEndSeq(); + } + } + + gg.translate(0, transY); + + drawIds(gg, av, ss, es, searchResults); + + gg.translate(0, -transY); + + fastPaint = true; + + // 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(); + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + */ + @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); + } + + gg = (Graphics2D) image.getGraphics(); + + // Fill in the background + gg.setColor(Color.white); + gg.fillRect(0, 0, getWidth(), imgHeight); + + drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults); + + g.drawImage(image, 0, 0, this); + } + + /** + * 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 g + * @param alignViewport + * @param startSeq + * @param endSeq + * @param selection + */ + void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq, + final int endSeq, List selection) + { + Font font = alignViewport.getFont(); + if (alignViewport.isSeqNameItalics()) + { + setIdfont(new Font(font.getName(), Font.ITALIC, + font.getSize())); + } + else + { + setIdfont(font); + } + + g.setFont(getIdfont()); + FontMetrics fm = g.getFontMetrics(); + + if (alignViewport.antiAlias) + { + g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + Color currentColor = Color.white; + Color currentTextColor = Color.black; + + boolean hasHiddenRows = alignViewport.hasHiddenRows(); + + if (alignViewport.getWrapAlignment()) + { + drawIdsWrapped(g, alignViewport, startSeq, getHeight()); + return; + } + + // Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; + + // Now draw the id strings + for (int i = startSeq; i <= endSeq; i++) + { + SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); + + if (sequence == null) + { + continue; + } + + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) + { + g.setFont(getHiddenFont(sequence, alignViewport)); + fm = g.getFontMetrics(); + } + + // 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)) + { + currentColor = Color.lightGray; + currentTextColor = Color.black; + } + else + { + currentColor = alignViewport.getSequenceColour(sequence); + currentTextColor = Color.black; + } + + g.setColor(currentColor); + + int charHeight = alignViewport.getCharHeight(); + g.fillRect(0, (i - startSeq) * charHeight, + getWidth(), charHeight); + + g.setColor(currentTextColor); + + String string = sequence + .getDisplayId(alignViewport.getShowJVSuffix()); + + if (alignViewport.isRightAlignIds()) + { + xPos = panelWidth - fm.stringWidth(string) - 4; + } + + g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); + + if (hasHiddenRows && av.getShowHiddenMarkers()) + { + drawMarker(g, alignViewport, i, startSeq, 0); + } + } + } + + /** + * 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(); + + /* + * assumption: SeqCanvas.calculateWrappedGeometry has been called + */ + SeqCanvas seqCanvas = alignViewport.getAlignPanel() + .getSeqPanel().seqCanvas; + + final int charHeight = alignViewport.getCharHeight(); + + AnnotationLabels labels = null; + if (alignViewport.isShowAnnotation()) + { + labels = new AnnotationLabels(alignViewport); + } + + ViewportRanges ranges = alignViewport.getRanges(); + + int rowSize = ranges.getViewportWidth(); + + /* + * 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()) + { + g.setFont(getHiddenFont(s, alignViewport)); + } + else + { + 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; + } + } + + /** + * 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 = alignViewport.getAlignment() + .getHiddenSequences().hiddenSequences; + // Use this method here instead of calling hiddenSeq adjust + // 3 times. + int hSize = hseqs.length; + + int hiddenIndex = seqIndex; + int lastIndex = seqIndex - 1; + int nextIndex = seqIndex + 1; + + for (int j = 0; j < hSize; j++) + { + if (hseqs[j] != null) + { + if (j - 1 < hiddenIndex) + { + hiddenIndex++; + } + if (j - 1 < lastIndex) + { + lastIndex++; + } + if (j - 1 < nextIndex) + { + nextIndex++; + } + } + } + + /* + * are we below or above the hidden sequences? + */ + boolean below = (hiddenIndex > lastIndex + 1); + boolean above = (nextIndex > hiddenIndex + 1); + + 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) + { + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset + charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); + } + if (above) + { + yShift++; + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset - charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); + } + } + + /** + * 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) + { + if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) + { + return new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); + } + return getIdfont(); + } + + /** + * DOCUMENT ME! + * + * @param list + * DOCUMENT ME! + */ + public void setHighlighted(List list) + { + searchResults = list; + repaint(); + } + + public Font getIdfont() + { + return idfont; + } + + public void setIdfont(Font idfont) + { + 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(); + } + } +}