X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=8623872ff550697490b6fcfc3e791e57ce448e5f;hb=91c5d2144a780716e755e99882acffe46b40f18f;hp=2b5995c7e3b72b74580c9bfda4e3f6aadb3a2985;hpb=8721f6e9e9c1df94142e2513236ffff084349fd3;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index 2b5995c..8623872 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -34,8 +34,8 @@ import javax.swing.*; */ public class SeqCanvas extends JComponent { - FeatureRenderer fr; - SequenceRenderer sr; + final FeatureRenderer fr; + final SequenceRenderer sr; BufferedImage img; Graphics2D gg; int imgWidth; @@ -46,6 +46,11 @@ public class SeqCanvas extends JComponent int LABEL_WEST; int LABEL_EAST; + + int cursorX = 0; + int cursorY = 0; + + /** * Creates a new SeqCanvas object. * @@ -128,9 +133,16 @@ public class SeqCanvas extends JComponent ypos += av.charHeight; if(av.hasHiddenColumns) - startx = av.getColumnSelection().adjustForHiddenColumns(startx); + { + startx = av.getColumnSelection().adjustForHiddenColumns(startx); + endx = av.getColumnSelection().adjustForHiddenColumns(endx); + } - // EAST SCALE + 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); @@ -175,15 +187,14 @@ public class SeqCanvas extends JComponent 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; - - while (index > startx) { if (jalview.util.Comparison.isGap(seq.getCharAt(index))) @@ -193,7 +204,7 @@ public class SeqCanvas extends JComponent continue; } - value = av.alignment.getSequenceAt(i).findPosition(index); + value = seq.findPosition(index); break; } @@ -342,7 +353,7 @@ public class SeqCanvas extends JComponent if (pdbCanvas != null) { - pdbCanvas.updateSeqColours(); + pdbCanvas.updateSeqColours(); } } @@ -400,19 +411,16 @@ 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()); } - int LABEL_WEST = 0; if (av.scaleLeftWrapped) { @@ -431,11 +439,22 @@ public class SeqCanvas extends JComponent av.endRes = av.startRes + cWidth; - int endx = (startRes + cWidth) - 1; + int endx; int ypos = hgap; + int maxwidth = av.alignment.getWidth(); - while ((ypos <= canvasHeight) && (startRes < 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); @@ -458,6 +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(); @@ -472,12 +520,6 @@ public class SeqCanvas extends JComponent cWidth * av.charWidth, (int) clip.getBounds().getHeight()); } - if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size()) - { - endx = av.vconsensus.size() - 2; - } - - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); if(av.showAnnotation) @@ -486,7 +528,7 @@ public class SeqCanvas extends JComponent if(annotations==null) annotations = new AnnotationPanel(av); - annotations.drawComponent( (Graphics2D) g, startRes, endx + 1); + annotations.drawComponent( (Graphics2D) g, startRes, endx+1); g.translate(0, -cHeight - ypos); } g.setClip(clip); @@ -497,12 +539,6 @@ public class SeqCanvas extends JComponent ypos -= 3; startRes += cWidth; - endx = (startRes + cWidth) - 1; - - if (endx > al.getWidth()) - { - endx = al.getWidth(); - } } } @@ -522,35 +558,12 @@ public class SeqCanvas extends JComponent * 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! */ - - float aaRatio = 2f/3f; - public void increaseAARatio() - { - aaRatio += .025; - if(aaRatio>1) - aaRatio = 1; - - repaint(); - } - - public void decreaseAARation() - { - aaRatio -= .025; - if(aaRatio<0) - aaRatio = 0; - - repaint(); - } - - void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, int endSeq, int offset) { @@ -584,15 +597,14 @@ public class SeqCanvas extends JComponent draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - g1.setColor(Color.blue); - g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, - startSeq + offset, - (blockEnd - blockStart + 1) * av.charWidth - 1, - startSeq + (endSeq - startSeq) * av.charHeight + offset); - g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth, - startSeq + offset, - (blockEnd - blockStart + 1) * av.charWidth, - startSeq + (endSeq - startSeq) * av.charHeight + offset); + if(av.getShowHiddenMarkers()) + { + g1.setColor(Color.blue); + g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1, + startSeq + offset, + (blockEnd - blockStart + 1) * av.charWidth - 1, + startSeq + (endSeq - startSeq) * av.charHeight + offset); + } g1.translate( -screenY * av.charWidth, 0); screenY += blockEnd - blockStart + 1; @@ -604,6 +616,7 @@ public class SeqCanvas extends JComponent blockEnd = blockStart + (endRes - startRes) - screenY; g1.translate(screenY * av.charWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); + g1.translate( -screenY * av.charWidth, 0); } } @@ -615,15 +628,13 @@ public class SeqCanvas extends JComponent //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 g1, + void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { - - sr.renderGaps(av.renderGaps); - Graphics2D g = (Graphics2D) g1; g.setFont(av.getFont()); + sr.prepare(g, av.renderGaps); SequenceI nextSeq; @@ -633,15 +644,14 @@ public class SeqCanvas extends JComponent { nextSeq = av.alignment.getSequenceAt(i); - sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), + sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes, offset + ( (i - startSeq) * av.charHeight)); if (av.showSequenceFeatures) { - fr.drawSequence(g1, nextSeq, startRes, endRes, - offset + ((i - startSeq) * 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 @@ -655,12 +665,29 @@ public class SeqCanvas extends JComponent sr.drawHighlightedText(nextSeq, visibleResults[r], visibleResults[r + 1], (visibleResults[r] - startRes) * av.charWidth, - offset + ( (i - startSeq) * av.charHeight), - av.charWidth, av.charHeight); + 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 @@ -701,11 +728,11 @@ public class SeqCanvas extends JComponent } if ( (sx <= (endRes-startRes)*av.charWidth) && - group.sequences.contains(av.alignment.getSequenceAt( - i))) + 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; @@ -714,7 +741,7 @@ 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; @@ -820,9 +847,13 @@ public class SeqCanvas extends JComponent } group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex); + + g.setStroke(new BasicStroke()); } while (groupIndex < av.alignment.getGroups().size()); + } + } /**