X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b4ef770883b7d6947dd810d688dd4d1666219b12;hb=c20e9d4ae9c98b093e74a10bf965e6d20d80fadf;hp=afb5a36e6262d79963dccdececf5749d8a214e0c;hpb=a6359c6eb746b06030b22135ed20417b971f580f;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index afb5a36..b4ef770 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -34,21 +34,23 @@ import javax.swing.*; */ public class SeqCanvas extends JComponent { - FeatureRenderer fr; - SequenceRenderer sr; + final FeatureRenderer fr; + final SequenceRenderer sr; BufferedImage img; Graphics2D gg; int imgWidth; int imgHeight; AlignViewport av; - boolean displaySearch = false; - int[] searchResults = null; - int chunkHeight; - int chunkWidth; + SearchResults searchResults = null; boolean fastPaint = false; int LABEL_WEST; int LABEL_EAST; + + int cursorX = 0; + int cursorY = 0; + + /** * Creates a new SeqCanvas object. * @@ -64,6 +66,28 @@ public class SeqCanvas extends JComponent setBackground(Color.white); } + MCview.PDBCanvas pdbCanvas; + public SequenceRenderer getSequenceRenderer() + { + return sr; + } + + public FeatureRenderer getFeatureRenderer() + { + return fr; + } + + public void setPDBCanvas(MCview.PDBCanvas pc) + { + pdbCanvas = pc; + } + + public AlignViewport getViewport() + { + return av; + } + + /** * DOCUMENT ME! * @@ -81,8 +105,11 @@ public class SeqCanvas extends JComponent // NORTH SCALE for (int i = scalestartx; i < endx; i += 10) { - String string = String.valueOf(i); - g.drawString(string, (i - startx - 1) * av.charWidth, + int value = i; + if(av.hasHiddenColumns) + value = av.getColumnSelection().adjustForHiddenColumns(value); + + g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth, ypos - (av.charHeight / 2)); g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2), @@ -105,7 +132,17 @@ public class SeqCanvas extends JComponent FontMetrics fm = getFontMetrics(av.getFont()); ypos += av.charHeight; - // EAST SCALE + if(av.hasHiddenColumns) + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } + + int maxwidth = av.alignment.getWidth(); + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + + // WEST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { SequenceI seq = av.alignment.getSequenceAt(i); @@ -147,10 +184,14 @@ public class SeqCanvas extends JComponent { ypos += av.charHeight; + if(av.hasHiddenColumns) + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + + SequenceI seq; // EAST SCALE for (int i = 0; i < av.alignment.getHeight(); i++) { - SequenceI seq = av.alignment.getSequenceAt(i); + seq = av.alignment.getSequenceAt(i); int index = endx; int value = -1; @@ -163,14 +204,14 @@ public class SeqCanvas extends JComponent continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = seq.findPosition(index); break; } if (value != -1) { - g.drawString(String.valueOf(value), av.charWidth/2, + g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) - (av.charHeight / 5)); } } @@ -184,13 +225,20 @@ public class SeqCanvas extends JComponent */ public void fastPaint(int horizontal, int vertical) { - if (((horizontal == 0) && (vertical == 0)) || (gg == null)) + if (gg == null) { return; } - gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth, - -vertical * av.charHeight); + + fastPaint = true; + + gg.copyArea(horizontal * av.charWidth, + vertical * av.charHeight, + imgWidth, + imgHeight, + -horizontal * av.charWidth, + -vertical * av.charHeight); int sr = av.startRes; int er = av.endRes; @@ -199,14 +247,16 @@ public class SeqCanvas extends JComponent int transX = 0; int transY = 0; + if (horizontal > 0) // scrollbar pulled right, image to the left { + er ++; transX = (er - sr - horizontal) * av.charWidth; sr = er - horizontal; } else if (horizontal < 0) { - er = sr - horizontal; + er = sr - horizontal-1; } else if (vertical > 0) // scroll down { @@ -232,14 +282,9 @@ public class SeqCanvas extends JComponent } gg.translate(transX, transY); - - gg.setColor(Color.white); - gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, - (es - ss) * av.charHeight); - drawPanel(gg, sr, er, ss, es, sr, ss, 0); + drawPanel(gg, sr, er, ss, es, 0); gg.translate(-transX, -transY); - fastPaint = true; repaint(); } @@ -257,16 +302,20 @@ public class SeqCanvas extends JComponent // Set this to false to force a full panel paint public void paintComponent(Graphics g) { - if ((img != null) && - (fastPaint || (getWidth() != g.getClipBounds().width) || - (getHeight() != g.getClipBounds().height))) + super.paintComponent(g); + + + + if ( img != null && (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height))) { g.drawImage(img, 0, 0, this); fastPaint = false; - return; } + // this draws the whole of the alignment imgWidth = getWidth(); imgHeight = getHeight(); @@ -282,17 +331,14 @@ public class SeqCanvas extends JComponent img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB); gg = (Graphics2D) img.getGraphics(); gg.setFont(av.getFont()); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + + if (av.antiAlias) + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, imgHeight); - chunkWidth = getWrappedCanvasWidth(getWidth()); - chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; - - av.setChunkHeight(chunkHeight); - av.setChunkWidth(chunkWidth); if (av.getWrapAlignment()) { @@ -300,11 +346,16 @@ public class SeqCanvas extends JComponent } else { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, - av.startRes, av.startSeq, 0); + drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); } g.drawImage(img, 0, 0, this); + + if (pdbCanvas != null) + { + pdbCanvas.updateSeqColours(); + } + } /** @@ -323,7 +374,7 @@ public class SeqCanvas extends JComponent if (av.scaleRightWrapped) { - LABEL_EAST = fm.stringWidth(getMask()+"0"); + LABEL_EAST = fm.stringWidth(getMask()); } if (av.scaleLeftWrapped) @@ -341,7 +392,7 @@ public class SeqCanvas extends JComponent */ String getMask() { - String mask = "0"; + String mask = "00"; for (int i = av.alignment.getWidth(); i > 0; i /= 10) { mask += "0"; @@ -360,35 +411,51 @@ public class SeqCanvas extends JComponent public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { - AlignmentI al = av.getAlignment(); FontMetrics fm = getFontMetrics(av.getFont()); - int LABEL_EAST = 0; if (av.scaleRightWrapped) { - LABEL_EAST = fm.stringWidth(getMask()+"0"); + LABEL_EAST = fm.stringWidth(getMask()); } - int LABEL_WEST = 0; if (av.scaleLeftWrapped) { LABEL_WEST = fm.stringWidth(getMask()); } + int hgap = av.charHeight; + if(av.scaleAboveWrapped) + hgap += av.charHeight; + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; - int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight; + int cHeight = av.getAlignment().getHeight() * av.charHeight; + + av.setWrappedWidth(cWidth); av.endRes = av.startRes + cWidth; - int endx = (startRes + cWidth) - 1; - int ypos = 2 * av.charHeight; - while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth())) + int endx; + int ypos = hgap; + int maxwidth = av.alignment.getWidth(); + + if(av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1; + + while ((ypos <= canvasHeight) && (startRes < maxwidth)) { + endx = startRes + cWidth -1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.setFont(av.getFont()); g.setColor(Color.black); if (av.scaleLeftWrapped) @@ -410,6 +477,35 @@ public class SeqCanvas extends JComponent drawNorthScale(g, startRes, endx, ypos); } + if (av.hasHiddenColumns && av.showHiddenMarkers) + { + g.setColor(Color.blue); + int res; + for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); + i++) + { + res = av.getColumnSelection().findHiddenRegionPosition(i) - + startRes; + + if (res < 0 || res > endx - startRes) + continue; + + gg.fillPolygon(new int[] + {res * av.charWidth - av.charHeight / 4, + res * av.charWidth + av.charHeight / 4, + res * av.charWidth}, + new int[] + { + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2), + ypos - (av.charHeight / 2) + 8 + }, 3); + + } + } + + + // When printing we have an extra clipped region, // the Printable page which we need to account for here Shape clip = g.getClip(); @@ -424,78 +520,190 @@ public class SeqCanvas extends JComponent cWidth * av.charWidth, (int) clip.getBounds().getHeight()); } - drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos); + drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + + if(av.showAnnotation) + { + g.translate(0, cHeight + ypos + 3); + if(annotations==null) + annotations = new AnnotationPanel(av); + + annotations.drawComponent( (Graphics2D) g, startRes, endx+1); + g.translate(0, -cHeight - ypos); + } g.setClip(clip); g.translate(-LABEL_WEST, 0); - ypos += cHeight; - startRes += cWidth; - endx = (startRes + cWidth) - 1; + ypos += cHeight+getAnnotationHeight()+hgap; + if(av.showAnnotation) + ypos -= 3; - if (endx > al.getWidth()) - { - endx = al.getWidth(); - } + startRes += cWidth; } } + AnnotationPanel annotations; + int getAnnotationHeight() + { + if(!av.showAnnotation) + return 0; + + if(annotations==null) + annotations = new AnnotationPanel(av); + + return annotations.adjustPanelHeight(); + } + /** * DOCUMENT ME! * * @param g1 DOCUMENT ME! - * @param x1 DOCUMENT ME! - * @param x2 DOCUMENT ME! - * @param y1 DOCUMENT ME! - * @param y2 DOCUMENT ME! - * @param startx DOCUMENT ME! - * @param starty DOCUMENT ME! + * @param startRes DOCUMENT ME! + * @param endRes DOCUMENT ME! + * @param startSeq DOCUMENT ME! + * @param endSeq DOCUMENT ME! * @param offset DOCUMENT ME! */ - synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1, - int y2, int startx, int starty, int offset) + void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) { - Graphics2D g = (Graphics2D) g1; - g.setFont(av.getFont()); - sr.renderGaps(av.renderGaps); + if(!av.hasHiddenColumns) + { + draw(g1, startRes, endRes, startSeq, endSeq, offset); + } + else + { + java.util.Vector regions = av.getColumnSelection().getHiddenColumns(); + + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int i = 0; i < regions.size(); i++) + { + int[] region = (int[]) regions.elementAt(i); + int hideStart = region[0]; + int hideEnd = region[1]; + + if (hideStart <= blockStart) + { + blockStart += (hideEnd - hideStart) + 1; + continue; + } - SequenceI nextSeq; + blockEnd = hideStart - 1; + + g1.translate(screenY * av.charWidth, 0); + + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + if(av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + 0+offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + (endSeq - startSeq) * av.charHeight + offset); + } + + g1.translate( -screenY * av.charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + } + + if (screenY <= (endRes - startRes)) + { + blockEnd = blockStart + (endRes - startRes) - screenY; + g1.translate(screenY * av.charWidth, 0); + draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + + g1.translate( -screenY * av.charWidth, 0); + } + } + + } + + + + + //int startRes, int endRes, int startSeq, int endSeq, int x, int y, + // int x1, int x2, int y1, int y2, int startx, int starty, + void draw(Graphics g, + int startRes, int endRes, + int startSeq, int endSeq, + int offset) + { + g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); + + SequenceI nextSeq; /// First draw the sequences ///////////////////////////// - for (int i = y1; i < y2; i++) + for (int i = startSeq; i < endSeq; i++) { nextSeq = av.alignment.getSequenceAt(i); - sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), - x1, x2, (x1 - startx) * av.charWidth, - offset + ((i - starty) * av.charHeight), av.charWidth, - av.charHeight); + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), + startRes, endRes, + offset + ( (i - startSeq) * av.charHeight)); if (av.showSequenceFeatures) { - fr.drawSequence(g, nextSeq, - av.alignment.findAllGroups(nextSeq), x1, x2, - (x1 - startx) * av.charWidth, - offset + ((i - starty) * av.charHeight), av.charWidth, - av.charHeight); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * av.charHeight)); } - } + /// Highlight search Results once all sequences have been drawn + ////////////////////////////////////////////////////////// + if (searchResults != null) + { + int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes); + if (visibleResults != null) + for (int r = 0; r < visibleResults.length; r += 2) + { + sr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], + (visibleResults[r] - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } + } + + if(av.cursorMode && cursorY==i + && cursorX>=startRes && cursorX<=endRes) + { + sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth, + offset + ( (i - startSeq) * av.charHeight)); + } + } + + if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0) + drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); + + } + + void drawGroupsBoundaries(Graphics g1, + int startRes, int endRes, + int startSeq, int endSeq, + int offset) + { + Graphics2D g = (Graphics2D)g1; // ///////////////////////////////////// // Now outline any areas if necessary ///////////////////////////////////// SequenceGroup group = av.getSelectionGroup(); - java.util.Vector groups = av.alignment.getGroups(); int sx = -1; int sy = -1; int ex = -1; int groupIndex = -1; + int visWidth = (endRes - startRes +1) * av.charWidth; - if ((group == null) && (groups.size() > 0)) + if ((group == null) && (av.alignment.getGroups().size() > 0)) { - group = (SequenceGroup) groups.elementAt(0); + group = (SequenceGroup) av.alignment.getGroups().elementAt(0); groupIndex = 0; } @@ -510,20 +718,24 @@ public class SeqCanvas extends JComponent int top = -1; int bottom = -1; - for (i = y1; i < y2; i++) + for (i = startSeq; i < endSeq; i++) { - sx = (group.getStartRes() - startx) * av.charWidth; - sy = offset + ((i - starty) * av.charHeight); + sx = (group.getStartRes() - startRes) * av.charWidth; + sy = offset + ((i - startSeq) * av.charHeight); ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; + if(sx+ex<0 || sx>visWidth) + { + continue; + } - if ((sx < (x2-x1)*av.charWidth) && - group.sequences.contains(av.alignment.getSequenceAt( - i))) + if ( (sx <= (endRes-startRes)*av.charWidth) && + group.getSequences(false). + contains(av.alignment.getSequenceAt(i))) { if ((bottom == -1) && - !group.sequences.contains( + !group.getSequences(false).contains( av.alignment.getSequenceAt(i + 1))) { bottom = sy + av.charHeight; @@ -532,7 +744,7 @@ public class SeqCanvas extends JComponent if (!inGroup) { if (((top == -1) && (i == 0)) || - !group.sequences.contains( + !group.getSequences(false).contains( av.alignment.getSequenceAt(i - 1))) { top = sy; @@ -558,95 +770,95 @@ public class SeqCanvas extends JComponent } else { - if (inGroup) + if (inGroup) + { + if (sx >= 0 && sx < visWidth) + g.drawLine(sx, oldY, sx, sy); + + if (sx + ex < visWidth) + g.drawLine(sx + ex, oldY, sx + ex, sy); + + if (sx < 0) { - g.drawLine(sx, oldY, sx, sy); - g.drawLine(sx + ex, oldY, sx + ex, sy); + ex += sx; + sx = 0; + } - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } + if (sx + ex > visWidth) + ex = visWidth; - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + ex = (endRes - startRes + 1) * av.charWidth; - inGroup = false; + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top = -1; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom, sx + ex, bottom); + bottom = -1; + } + + inGroup = false; } } } - if (inGroup) { - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; - } - - sy = offset + ((i - starty) * av.charHeight); + sy = offset + ( (i - startSeq) * av.charHeight); + if (sx >= 0 && sx < visWidth) g.drawLine(sx, oldY, sx, sy); + + if (sx + ex < visWidth) g.drawLine(sx + ex, oldY, sx + ex, sy); + + if (sx < 0) + { + ex += sx; + sx = 0; + } + + if (sx + ex > visWidth) + ex = visWidth; + else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) + ex = (endRes - startRes + 1) * av.charWidth; + + if (top != -1) + { + g.drawLine(sx, top, sx + ex, top); + top = -1; + } + + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + bottom = -1; + } + inGroup = false; } groupIndex++; - if (groupIndex >= groups.size()) + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.alignment.getGroups().size()) { break; } - group = (SequenceGroup) groups.elementAt(groupIndex); - } - while (groupIndex < groups.size()); - } - - /// Highlight search Results once all sequences have been drawn - ////////////////////////////////////////////////////////// - if (displaySearch) - { - for (int r = 0; r < searchResults.length; r += 3) - { - int searchSeq = searchResults[r]; - - if ((searchSeq >= y1) && (searchSeq < y2)) - { - SequenceI seq = av.getAlignment().getSequenceAt(searchSeq); - - int searchStart = seq.findIndex(searchResults[r + 1]) - 1; - int searchEnd = seq.findIndex(searchResults[r + 2]) - 1; + group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); - SequenceRenderer ssr = (SequenceRenderer) sr; - if (searchStart < x1) - { - searchStart = x1; - } - - if (searchEnd > x2) - { - searchEnd = x2; - } - - ssr.drawHighlightedText(seq, searchStart, searchEnd, - (searchStart - startx) * av.charWidth, - offset + ((searchSeq - starty) * av.charHeight), - av.charWidth, av.charHeight); - } } + while (groupIndex < av.alignment.getGroups().size()); + } + } /** @@ -654,17 +866,9 @@ public class SeqCanvas extends JComponent * * @param results DOCUMENT ME! */ - public void highlightSearchResults(int[] results) + public void highlightSearchResults(SearchResults results) { - // results are in the order sequence, startRes, endRes - if (results == null) - { - displaySearch = false; - } - else - { - displaySearch = true; - } + img = null; searchResults = results;