X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=9c2fd7393c8c10d37107a1acbccd10f0f0802e88;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=5afbe234b99f75a39aca0eff325866f1c425abe2;hpb=dc086b020537a18c3ce575fbb220033979270a65;p=jalview.git
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5afbe23..9c2fd73 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,646 +1,827 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class SeqCanvas
- extends Panel
-{
- FeatureRenderer fr;
- SequenceRenderer sr;
- Image img;
- Graphics gg;
- int imgWidth;
- int imgHeight;
-
- AlignViewport av;
-
- SearchResults searchResults = null;
-
- int chunkHeight;
- int chunkWidth;
-
- boolean fastPaint = false;
-
-
- public SeqCanvas(AlignViewport av)
- {
- this.av = av;
- fr = new FeatureRenderer(av);
- sr = new SequenceRenderer(av);
- PaintRefresher.Register(this, av.alignment);
- }
-
- public AlignViewport getViewport()
- {
- return av;
- }
-
- public FeatureRenderer getFeatureRenderer()
- {
- return fr;
- }
-
- MCview.AppletPDBCanvas pdbCanvas;
- public SequenceRenderer getSequenceRenderer()
- {
- return sr;
- }
-
- public void setPDBCanvas(MCview.AppletPDBCanvas pc)
- {
- pdbCanvas = pc;
- }
-
-
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
- {
- int scalestartx = startx - startx % 10 + 10;
-
- g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
- {
- String string = String.valueOf(i);
- g.drawString(string, (i - startx - 1) * av.charWidth,
- ypos - av.charHeight / 2);
-
- g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
- ypos + 2 - av.charHeight / 2,
- (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
-
- }
- }
-
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
- // EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI seq = av.alignment.getSequenceAt(i);
- int index = startx;
- int value = -1;
- while (index < endx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index++;
- continue;
- }
-
- value = av.alignment.getSequenceAt(i).findPosition(index);
- break;
- }
- if (value != -1)
- {
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
- g.drawString(value + "", x,
- ypos + i * av.charHeight - av.charHeight / 5);
- }
- }
- }
-
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
- {
- ypos += av.charHeight;
- // EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceI seq = av.alignment.getSequenceAt(i);
- int index = endx;
- int value = -1;
- while (index > startx)
- {
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
- {
- index--;
- continue;
- }
-
- value = av.alignment.getSequenceAt(i).findPosition(index);
- break;
- }
- if (value != -1)
- {
- g.drawString(value + "", av.charWidth/2,
- ypos + i * av.charHeight - av.charHeight / 5);
- }
- }
-
- }
-
- int lastsr=0;
- void fastPaint(int horizontal, int vertical)
- {
- if ( fastPaint || gg == null)
- {
- return;
- }
-
-
- // Its possible on certain browsers that the call to fastpaint
- // is faster than it can paint, so this check here catches
- // this possibility
- if(lastsr + horizontal != av.startRes)
- {
- horizontal = av.startRes - lastsr;
- }
-
- lastsr = av.startRes;
-
- fastPaint = true;
- gg.copyArea(horizontal * av.charWidth,
- vertical * av.charHeight,
- imgWidth - horizontal * av.charWidth,
- imgHeight - vertical * av.charHeight,
- -horizontal * av.charWidth,
- -vertical * av.charHeight);
-
-
-
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
- transX = 0, transY = 0;
-
- if (horizontal > 0) // scrollbar pulled right, image to the left
- {
- transX = (er - sr - horizontal) * av.charWidth;
- sr = er - horizontal;
- }
- else if (horizontal < 0)
- {
- er = sr - horizontal;
- }
-
- else if (vertical > 0) // scroll down
- {
- ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
- {
- ss = av.startSeq;
- }
- else
- {
- transY = imgHeight - vertical * av.charHeight;
- }
- }
- else if (vertical < 0)
- {
- es = ss - vertical;
- if (es > av.endSeq)
- {
- es = av.endSeq;
- }
- }
-
- gg.translate(transX, transY);
-
- drawPanel(gg, sr, er, ss, es, 0);
- gg.translate( -transX, -transY);
-
- repaint();
-
- }
-
- /**
- * Definitions of startx and endx (hopefully):
- * SMJS This is what I'm working towards!
- * startx is the first residue (starting at 0) to display.
- * endx is the last residue to display (starting at 0).
- * starty is the first sequence to display (starting at 0).
- * endy is the last sequence to display (starting at 0).
- * NOTE 1: The av limits are set in setFont in this class and
- * in the adjustment listener in SeqPanel when the scrollbars move.
- */
- public void update(Graphics g)
- {
- paint(g);
- }
-
- public void paint(Graphics g)
- {
-
- if (fastPaint)
- {
- g.drawImage(img, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- // this draws the whole of the alignment
- imgWidth = this.getSize().width;
- imgHeight = this.getSize().height;
-
- imgWidth -= imgWidth % av.charWidth;
- imgHeight -= imgHeight % av.charHeight;
-
- if (imgWidth < 1 || imgHeight < 1)
- {
- return;
- }
-
- if (img == null || imgWidth != img.getWidth(this) ||
- imgHeight != img.getHeight(this))
- {
- img = createImage(imgWidth, imgHeight);
- gg = img.getGraphics();
- gg.setFont(av.getFont());
- }
-
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
-
-
- if (av.getWrapAlignment())
- {
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
- }
- else
- {
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
- }
-
- g.drawImage(img, 0, 0, this);
-
- if (pdbCanvas != null)
- {
- pdbCanvas.updateSeqColours();
- }
- }
-
- int LABEL_WEST, LABEL_EAST;
- public int getWrappedCanvasWidth(int cwidth)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
-
- LABEL_EAST = 0;
- LABEL_WEST = 0;
-
- if (av.scaleRightWrapped)
- {
- LABEL_EAST = fm.stringWidth(getMask());
- }
-
- if (av.scaleLeftWrapped)
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- }
-
-
- /**
- * Generates a string of zeroes.
- * @return String
- */
- String getMask()
- {
- String mask = "00";
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)
- {
- mask += "0";
- }
- return mask;
- }
-
- 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)
- {
- 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() * av.charHeight;
-
- av.setWrappedWidth(cWidth);
-
- av.endRes = av.startRes + cWidth;
-
-
- int endx = (startRes + cWidth) - 1;
- int ypos = hgap;
-
-
- while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
- {
- g.setColor(Color.black);
-
- if (av.scaleLeftWrapped)
- {
- drawWestScale(g, startRes, endx, ypos);
- }
-
- if (av.scaleRightWrapped)
- {
- g.translate(canvasWidth - LABEL_EAST, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
- }
-
- g.translate(LABEL_WEST, 0);
-
- if (av.scaleAboveWrapped)
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
-
-
- if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
- {
- endx = av.vconsensus.size() - 2;
- }
-
-
- if(g.getClip()==null)
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
-
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
- g.setClip(null);
-
-
- if(av.showAnnotation)
- {
- g.translate(0, cHeight + ypos+4);
- if(annotations==null)
- annotations = new AnnotationPanel(av);
-
- annotations.drawComponent( g, startRes, endx + 1);
- g.translate(0, -cHeight - ypos-4);
- }
- g.translate(-LABEL_WEST, 0);
-
- ypos += cHeight+getAnnotationHeight()+hgap;
-
-
- startRes += cWidth;
- endx = (startRes + cWidth) - 1;
-
- if (endx > al.getWidth())
- {
- endx = al.getWidth();
- }
- }
-
- }
-
- AnnotationPanel annotations;
- int getAnnotationHeight()
- {
- if(!av.showAnnotation)
- return 0;
-
- if(annotations==null)
- annotations = new AnnotationPanel(av);
-
- return annotations.adjustPanelHeight();
- }
-
- void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)
- {
-
- g.setFont(av.getFont());
- sr.renderGaps(av.renderGaps);
-
- SequenceI nextSeq;
- /// First draw the sequences
- /////////////////////////////
- for (int i = startSeq; i < endSeq; i++)
- {
- nextSeq = av.alignment.getSequenceAt(i);
-
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,
- offset + ( (i - startSeq) * av.charHeight));
-
- if (av.showSequenceFeatures)
- {
- fr.drawSequence(g, nextSeq, startRes, endRes,
- offset + ((i - startSeq) * av.charHeight),
- av.charWidth, 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),
- av.charWidth, av.charHeight);
- }
- }
- }
-
- //
- /////////////////////////////////////
- // Now outline any areas if necessary
- /////////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
-
- int sx = -1;
- int sy = -1;
- int ex = -1;
- int groupIndex = -1;
-
- if ((group == null) && (av.alignment.getGroups().size() > 0))
- {
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
- groupIndex = 0;
- }
-
- if ( group != null)
- {
- do
- {
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
-
- for (i = startSeq; i < endSeq; i++)
- {
- 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>imgWidth)
- {
- continue;
- }
-
- if ( (sx <= (endRes-startRes)*av.charWidth) &&
- group.sequences.contains(av.alignment.getSequenceAt(
- i)))
- {
- if (bottom == -1)
- {
- if(i == endSeq-1 || // Dont check for i+1 if on the bottom row
- !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))
-
- bottom = sy + av.charHeight;
- }
-
- if (!inGroup)
- {
- if (((top == -1) && (i == 0)) ||
- !group.sequences.contains(
- av.alignment.getSequenceAt(i - 1)))
- {
- top = sy;
- }
-
- oldY = sy;
- inGroup = true;
-
- if (group == av.getSelectionGroup())
- {
- g.setColor(Color.red);
- }
- else
- {
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
- {
- if (inGroup)
- {
- if (sx >= 0 && sx < imgWidth)
- g.drawLine(sx, oldY, sx, sy);
-
- if (sx + ex < imgWidth)
- g.drawLine(sx + ex, oldY, sx + ex, sy);
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > imgWidth)
- ex = imgWidth;
-
- 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, sx + ex, bottom);
- bottom = -1;
- }
-
- inGroup = false;
- }
- }
- }
-
- if (inGroup)
- {
- sy = offset + ( (i - startSeq) * av.charHeight);
- if (sx >= 0 && sx < imgWidth)
- g.drawLine(sx, oldY, sx, sy);
-
- if (sx + ex < imgWidth)
- g.drawLine(sx + ex, oldY, sx + ex, sy);
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > imgWidth)
- ex = imgWidth;
- 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 >= av.alignment.getGroups().size())
- {
- break;
- }
-
- group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
- }
- while (groupIndex < av.alignment.getGroups().size());
- }
- }
-
- public void highlightSearchResults(SearchResults results)
- {
- searchResults = results;
-
- repaint();
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.util.List;
+
+public class SeqCanvas extends Panel
+{
+ FeatureRenderer fr;
+
+ SequenceRenderer sr;
+
+ Image img;
+
+ Graphics gg;
+
+ int imgWidth;
+
+ int imgHeight;
+
+ AlignViewport av;
+
+ SearchResults searchResults = null;
+
+ boolean fastPaint = false;
+
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ public SeqCanvas(AlignViewport av)
+ {
+ this.av = av;
+ fr = new FeatureRenderer(av);
+ sr = new SequenceRenderer(av);
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return fr;
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return sr;
+ }
+
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ {
+ int scalestartx = startx - startx % 10 + 10;
+
+ g.setColor(Color.black);
+
+ // NORTH SCALE
+ for (int i = scalestartx; i < endx; i += 10)
+ {
+ 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),
+ (ypos + 2) - (av.charHeight / 2),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ ypos - 2);
+ }
+ }
+
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += av.charHeight;
+ if (av.hasHiddenColumns())
+ {
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ // WEST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
+ int index = startx;
+ int value = -1;
+
+ while (index < endx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index++;
+
+ continue;
+ }
+
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ - av.charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * av.charHeight))
+ - (av.charHeight / 5));
+ }
+ }
+ }
+
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += av.charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ int index = endx;
+ int value = -1;
+
+ while (index > startx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index--;
+
+ continue;
+ }
+
+ value = seq.findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
+ - (av.charHeight / 5));
+ }
+ }
+ }
+
+ int lastsr = 0;
+
+ void fastPaint(int horizontal, int vertical)
+ {
+ if (fastPaint || gg == null)
+ {
+ return;
+ }
+
+ // Its possible on certain browsers that the call to fastpaint
+ // is faster than it can paint, so this check here catches
+ // this possibility
+ if (lastsr + horizontal != av.startRes)
+ {
+ horizontal = av.startRes - lastsr;
+ }
+
+ lastsr = av.startRes;
+
+ fastPaint = true;
+ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
+ imgWidth - horizontal * av.charWidth, imgHeight - vertical
+ * av.charHeight, -horizontal * av.charWidth, -vertical
+ * av.charHeight);
+
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * av.charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+
+ else if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ {
+ ss = av.startSeq;
+ }
+ else
+ {
+ transY = imgHeight - vertical * av.charHeight;
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(transX, transY);
+
+ drawPanel(gg, sr, er, ss, es, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
+
+ }
+
+ /**
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+ * towards! startx is the first residue (starting at 0) to display. endx is
+ * the last residue to display (starting at 0). starty is the first sequence
+ * to display (starting at 0). endy is the last sequence to display (starting
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+ * adjustment listener in SeqPanel when the scrollbars move.
+ */
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+
+ if (img != null
+ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
+ .getClipBounds().height)))
+ {
+ g.drawImage(img, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ if (fastPaint)
+ {
+ g.drawImage(img, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ // this draws the whole of the alignment
+ imgWidth = this.getSize().width;
+ imgHeight = this.getSize().height;
+
+ imgWidth -= imgWidth % av.charWidth;
+ imgHeight -= imgHeight % av.charHeight;
+
+ if (imgWidth < 1 || imgHeight < 1)
+ {
+ return;
+ }
+
+ if (img == null || imgWidth != img.getWidth(this)
+ || imgHeight != img.getHeight(this))
+ {
+ img = createImage(imgWidth, imgHeight);
+ gg = img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, imgHeight);
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ }
+ else
+ {
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ }
+
+ g.drawImage(img, 0, 0, this);
+
+ }
+
+ int LABEL_WEST, LABEL_EAST;
+
+ public int getWrappedCanvasWidth(int cwidth)
+ {
+ cwidth -= cwidth % av.charWidth;
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.scaleRightWrapped)
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.scaleLeftWrapped)
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ }
+
+ /**
+ * Generates a string of zeroes.
+ *
+ * @return String
+ */
+ String getMask()
+ {
+ String mask = "0";
+ int maxWidth = 0;
+ int tmp;
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ tmp = alignment.getSequenceAt(i).getEnd();
+ if (tmp > maxWidth)
+ {
+ maxWidth = tmp;
+ }
+ }
+
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ mask += "0";
+ }
+ return mask;
+ }
+
+ public void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ AlignmentI al = av.getAlignment();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ if (av.scaleRightWrapped)
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ 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() * av.charHeight;
+
+ av.setWrappedWidth(cWidth);
+
+ av.endRes = av.startRes + cWidth;
+
+ int endx;
+ int ypos = hgap;
+
+ int maxwidth = av.getAlignment().getWidth() - 1;
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
+ {
+ endx = startRes + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.setColor(Color.black);
+
+ if (av.scaleLeftWrapped)
+ {
+ drawWestScale(g, startRes, endx, ypos);
+ }
+
+ if (av.scaleRightWrapped)
+ {
+ g.translate(canvasWidth - LABEL_EAST, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ if (av.scaleAboveWrapped)
+ {
+ 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);
+
+ }
+ }
+
+ if (g.getClip() == null)
+ {
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ g.setClip(null);
+
+ if (av.showAnnotation)
+ {
+ g.translate(0, cHeight + ypos + 4);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.drawComponent(g, startRes, endx + 1);
+ g.translate(0, -cHeight - ypos - 4);
+ }
+ g.translate(-LABEL_WEST, 0);
+
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ startRes += cWidth;
+ }
+
+ }
+
+ AnnotationPanel annotations;
+
+ int getAnnotationHeight()
+ {
+ if (!av.showAnnotation)
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
+ {
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ }
+ else
+ {
+ List regions = av.getColumnSelection().getHiddenColumns();
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : regions)
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ 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 = startSeq; i < endSeq; i++)
+ {
+ nextSeq = av.getAlignment().getSequenceAt(i);
+
+ if (nextSeq == null)
+ {
+ continue;
+ }
+
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+
+ if (av.showSequenceFeatures)
+ {
+ 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.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+ SequenceGroup group = av.getSelectionGroup();
+
+ int sx = -1;
+ int sy = -1;
+ int ex = -1;
+ int groupIndex = -1;
+
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ {
+ group = av.getAlignment().getGroups().get(0);
+ groupIndex = 0;
+ }
+
+ if (group != null)
+ {
+ do
+ {
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+ int alHeight = av.getAlignment().getHeight() - 1;
+
+ for (i = startSeq; i < endSeq; i++)
+ {
+ 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 > imgWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * av.charWidth)
+ && group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && (i >= alHeight || !group.getSequences(null)
+ .contains(
+ av.getAlignment().getSequenceAt(i + 1))))
+ {
+ bottom = sy + av.charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0))
+ || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
+
+ if (group == av.getSelectionGroup())
+ {
+ g.setColor(Color.red);
+ }
+ else
+ {
+ g.setColor(group.getOutlineColour());
+ }
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ if (sx >= 0 && sx < imgWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < imgWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > imgWidth)
+ {
+ ex = imgWidth;
+ }
+
+ 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, sx + ex, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+
+ if (inGroup)
+ {
+ sy = offset + ((i - startSeq) * av.charHeight);
+ if (sx >= 0 && sx < imgWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < imgWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > imgWidth)
+ {
+ ex = imgWidth;
+ }
+ 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 >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups()
+ .get(groupIndex);
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+ }
+
+ public void highlightSearchResults(SearchResults results)
+ {
+ searchResults = results;
+
+ repaint();
+ }
+
+}