-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
- * 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 jalview.util.Comparison;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.Color;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Image;
-
-import javax.swing.JPanel;
-
-public class SeqCanvas extends JPanel
-{
- 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());
- updateViewport();
- }
-
- int avcharHeight = 0, avcharWidth = 0;
-
- private void updateViewport()
- {
- avcharHeight = av.getCharHeight();
- avcharWidth = av.getCharWidth();
- }
-
- public AlignmentViewport getViewport()
- {
- return av;
- }
-
- public FeatureRenderer getFeatureRenderer()
- {
- return fr;
- }
-
- public SequenceRenderer getSequenceRenderer()
- {
- return sr;
- }
-
- private 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) * avcharWidth,
- ypos - (avcharHeight / 2));
-
- g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- (ypos + 2) - (avcharHeight / 2),
- ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
- ypos - 2);
- }
- }
-
- private void drawWestScale(Graphics g, int startx, int endx, int ypos)
- {
- FontMetrics fm = getFontMetrics(av.getFont());
- ypos += avcharHeight;
- 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 (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))
- - avcharWidth / 2;
- g.drawString(value + "", x, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
- }
- }
- }
-
- private void drawEastScale(Graphics g, int startx, int endx, int ypos)
- {
- ypos += avcharHeight;
-
- 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 (Comparison.isGap(seq.getCharAt(index)))
- {
- index--;
-
- continue;
- }
-
- value = seq.findPosition(index);
-
- break;
- }
-
- if (value != -1)
- {
- g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
- - (avcharHeight / 5));
- }
- }
- }
-
- int lastsr = 0;
-
- void fastPaint(int horizontal, int vertical)
- {
- if (fastPaint || gg == null)
- {
- return;
- }
-
- updateViewport();
-
- // 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 * avcharWidth, vertical * avcharHeight, imgWidth
- - horizontal * avcharWidth,
- imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
- -vertical * avcharHeight);
-
- 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) * avcharWidth;
- 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 * avcharHeight;
- }
- }
- 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);
- }
-
- @Override
- 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;
- }
-
- updateViewport();
- // this draws the whole of the alignment
- imgWidth = this.getSize().width;
- imgHeight = this.getSize().height;
-
- imgWidth -= imgWidth % avcharWidth;
- imgHeight -= imgHeight % avcharHeight;
-
- 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.getCharWidth();
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- LABEL_EAST = 0;
- LABEL_WEST = 0;
-
- if (av.getScaleRightWrapped())
- {
- LABEL_EAST = fm.stringWidth(getMask());
- }
-
- if (av.getScaleLeftWrapped())
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
- }
-
- /**
- * 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;
- }
-
- private void drawWrappedPanel(Graphics g, int canvasWidth,
- int canvasHeight, int startRes)
- {
- AlignmentI al = av.getAlignment();
-
- FontMetrics fm = getFontMetrics(av.getFont());
-
- if (av.getScaleRightWrapped())
- {
- LABEL_EAST = fm.stringWidth(getMask());
- }
-
- if (av.getScaleLeftWrapped())
- {
- LABEL_WEST = fm.stringWidth(getMask());
- }
-
- int hgap = avcharHeight;
- if (av.getScaleAboveWrapped())
- {
- hgap += avcharHeight;
- }
-
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
- int cHeight = av.getAlignment().getHeight() * avcharHeight;
-
- 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.getScaleLeftWrapped())
- {
- drawWestScale(g, startRes, endx, ypos);
- }
-
- if (av.getScaleRightWrapped())
- {
- g.translate(canvasWidth - LABEL_EAST, 0);
- drawEastScale(g, startRes, endx, ypos);
- g.translate(-(canvasWidth - LABEL_EAST), 0);
- }
-
- g.translate(LABEL_WEST, 0);
-
- if (av.getScaleAboveWrapped())
- {
- drawNorthScale(g, startRes, endx, ypos);
- }
- if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
- {
- 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 * avcharWidth - avcharHeight / 4,
- res * avcharWidth + avcharHeight / 4, res * avcharWidth },
- new int[]
- { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
- ypos - (avcharHeight / 2) + 8 }, 3);
-
- }
- }
-
- if (g.getClip() == null)
- {
- g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
- }
-
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
- g.setClip(null);
-
- if (av.isShowAnnotation())
- {
- 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.isShowAnnotation())
- {
- return 0;
- }
-
- if (annotations == null)
- {
- annotations = new AnnotationPanel(av);
- }
-
- return annotations.adjustPanelHeight();
- }
-
- private 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
- {
-
- int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
-
- if (av.hasHiddenColumns())
- {
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- blockEnd = hideStart - 1;
-
- g1.translate(screenY * avcharWidth, 0);
-
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- if (av.getShowHiddenMarkers())
- {
- g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
- - 1, (endSeq - startSeq) * avcharHeight
- + offset);
- }
-
- g1.translate(-screenY * avcharWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
- }
- }
- if (screenY <= (endRes - startRes))
- {
- blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * avcharWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- g1.translate(-screenY * avcharWidth, 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.isRenderGaps());
- updateViewport();
- 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) * avcharHeight));
-
- if (av.isShowSequenceFeatures())
- {
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * avcharHeight));
- }
-
- // / 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)
- * avcharWidth, offset
- + ((i - startSeq) * avcharHeight));
- }
- }
- }
-
- if (av.cursorMode && cursorY == i && cursorX >= startRes
- && cursorX <= endRes)
- {
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
- offset + ((i - startSeq) * avcharHeight));
- }
- }
-
- if (av.getSelectionGroup() != null
- || av.getAlignment().getGroups().size() > 0)
- {
- drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
- }
-
- }
-
- private 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) * avcharWidth;
- sy = offset + ((i - startSeq) * avcharHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
-
- if (sx + ex < 0 || sx > imgWidth)
- {
- continue;
- }
-
- if ((sx <= (endRes - startRes) * avcharWidth)
- && group.getSequences(null).contains(
- av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1)
- && (i >= alHeight || !group.getSequences(null)
- .contains(
- av.getAlignment().getSequenceAt(i + 1))))
- {
- bottom = sy + avcharHeight;
- }
-
- 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) * avcharWidth)
- {
- ex = (endRes - startRes + 1) * avcharWidth;
- }
-
- 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) * avcharHeight);
- 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) * avcharWidth)
- {
- ex = (endRes - startRes + 1) * avcharWidth;
- }
-
- 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();
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.util.Comparison;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import java.awt.Color;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+import java.awt.Image;\r
+\r
+import javax.swing.JPanel;\r
+\r
+public class SeqCanvas extends JPanel\r
+{\r
+ FeatureRenderer fr;\r
+\r
+ SequenceRenderer sr;\r
+\r
+ Image img;\r
+\r
+ Graphics gg;\r
+\r
+ int imgWidth;\r
+\r
+ int imgHeight;\r
+\r
+ AlignViewport av;\r
+\r
+ SearchResults searchResults = null;\r
+\r
+ boolean fastPaint = false;\r
+\r
+ int cursorX = 0;\r
+\r
+ int cursorY = 0;\r
+\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+ updateViewport();\r
+ }\r
+\r
+ int avcharHeight = 0, avcharWidth = 0;\r
+\r
+ private void updateViewport()\r
+ {\r
+ avcharHeight = av.getCharHeight();\r
+ avcharWidth = av.getCharWidth();\r
+ }\r
+\r
+ public AlignmentViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ int scalestartx = startx - startx % 10 + 10;\r
+\r
+ g.setColor(Color.black);\r
+\r
+ // NORTH SCALE\r
+ for (int i = scalestartx; i < endx; i += 10)\r
+ {\r
+ int value = i;\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+ }\r
+\r
+ g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,\r
+ ypos - (avcharHeight / 2));\r
+\r
+ g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),\r
+ (ypos + 2) - (avcharHeight / 2),\r
+ ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),\r
+ ypos - 2);\r
+ }\r
+ }\r
+\r
+ private void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ ypos += avcharHeight;\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ int maxwidth = av.getAlignment().getWidth();\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ // WEST SCALE\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.getAlignment().getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
+\r
+ while (index < endx)\r
+ {\r
+ if (Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index++;\r
+\r
+ continue;\r
+ }\r
+\r
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))\r
+ - avcharWidth / 2;\r
+ g.drawString(value + "", x, (ypos + (i * avcharHeight))\r
+ - (avcharHeight / 5));\r
+ }\r
+ }\r
+ }\r
+\r
+ private void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ ypos += avcharHeight;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ SequenceI seq;\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+ {\r
+ seq = av.getAlignment().getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
+\r
+ while (index > startx)\r
+ {\r
+ if (Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+\r
+ continue;\r
+ }\r
+\r
+ value = seq.findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\r
+ g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))\r
+ - (avcharHeight / 5));\r
+ }\r
+ }\r
+ }\r
+\r
+ int lastsr = 0;\r
+\r
+ void fastPaint(int horizontal, int vertical)\r
+ {\r
+ if (fastPaint || gg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ updateViewport();\r
+\r
+ // Its possible on certain browsers that the call to fastpaint\r
+ // is faster than it can paint, so this check here catches\r
+ // this possibility\r
+ if (lastsr + horizontal != av.startRes)\r
+ {\r
+ horizontal = av.startRes - lastsr;\r
+ }\r
+\r
+ lastsr = av.startRes;\r
+\r
+ fastPaint = true;\r
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth\r
+ - horizontal * avcharWidth,\r
+ imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,\r
+ -vertical * avcharHeight);\r
+\r
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;\r
+\r
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * avcharWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
+\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ {\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - vertical * avcharHeight;\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
+\r
+ gg.translate(transX, transY);\r
+\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
+ gg.translate(-transX, -transY);\r
+\r
+ repaint();\r
+\r
+ }\r
+\r
+ /**\r
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working\r
+ * towards! startx is the first residue (starting at 0) to display. endx is\r
+ * the last residue to display (starting at 0). starty is the first sequence\r
+ * to display (starting at 0). endy is the last sequence to display (starting\r
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the\r
+ * adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
+\r
+ @Override\r
+ public void paint(Graphics g)\r
+ {\r
+\r
+ if (img != null\r
+ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g\r
+ .getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
+ if (fastPaint)\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
+ updateViewport();\r
+ // this draws the whole of the alignment\r
+ imgWidth = this.getSize().width;\r
+ imgHeight = this.getSize().height;\r
+\r
+ imgWidth -= imgWidth % avcharWidth;\r
+ imgHeight -= imgHeight % avcharHeight;\r
+\r
+ if (imgWidth < 1 || imgHeight < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (img == null || imgWidth != img.getWidth(this)\r
+ || imgHeight != img.getHeight(this))\r
+ {\r
+ img = createImage(imgWidth, imgHeight);\r
+ gg = img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }\r
+\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
+ }\r
+ else\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
+ }\r
+\r
+ g.drawImage(img, 0, 0, this);\r
+\r
+ }\r
+\r
+ int LABEL_WEST, LABEL_EAST;\r
+\r
+ public int getWrappedCanvasWidth(int cwidth)\r
+ {\r
+ cwidth -= cwidth % av.getCharWidth();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
+\r
+ if (av.getScaleRightWrapped())\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ if (av.getScaleLeftWrapped())\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();\r
+ }\r
+\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * \r
+ * @return String\r
+ */\r
+ String getMask()\r
+ {\r
+ String mask = "0";\r
+ int maxWidth = 0;\r
+ int tmp;\r
+ AlignmentI alignment = av.getAlignment();\r
+ for (int i = 0; i < alignment.getHeight(); i++)\r
+ {\r
+ tmp = alignment.getSequenceAt(i).getEnd();\r
+ if (tmp > maxWidth)\r
+ {\r
+ maxWidth = tmp;\r
+ }\r
+ }\r
+\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
+ }\r
+\r
+ private void drawWrappedPanel(Graphics g, int canvasWidth,\r
+ int canvasHeight, int startRes)\r
+ {\r
+ AlignmentI al = av.getAlignment();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ if (av.getScaleRightWrapped())\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ if (av.getScaleLeftWrapped())\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ int hgap = avcharHeight;\r
+ if (av.getScaleAboveWrapped())\r
+ {\r
+ hgap += avcharHeight;\r
+ }\r
+\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;\r
+ int cHeight = av.getAlignment().getHeight() * avcharHeight;\r
+\r
+ av.setWrappedWidth(cWidth);\r
+\r
+ av.endRes = av.startRes + cWidth;\r
+\r
+ int endx;\r
+ int ypos = hgap;\r
+\r
+ int maxwidth = av.getAlignment().getWidth() - 1;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
+ {\r
+ endx = startRes + cWidth - 1;\r
+\r
+ if (endx > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
+\r
+ g.setColor(Color.black);\r
+\r
+ if (av.getScaleLeftWrapped())\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
+\r
+ if (av.getScaleRightWrapped())\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
+ }\r
+\r
+ g.translate(LABEL_WEST, 0);\r
+\r
+ if (av.getScaleAboveWrapped())\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())\r
+ {\r
+ g.setColor(Color.blue);\r
+ int res;\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
+ {\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i)\r
+ - startRes;\r
+\r
+ if (res < 0 || res > endx - startRes)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ gg.fillPolygon(new int[]\r
+ { res * avcharWidth - avcharHeight / 4,\r
+ res * avcharWidth + avcharHeight / 4, res * avcharWidth },\r
+ new int[]\r
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),\r
+ ypos - (avcharHeight / 2) + 8 }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ if (g.getClip() == null)\r
+ {\r
+ g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);\r
+ }\r
+\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+ g.setClip(null);\r
+\r
+ if (av.isShowAnnotation())\r
+ {\r
+ g.translate(0, cHeight + ypos + 4);\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ annotations.drawComponent(g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos - 4);\r
+ }\r
+ g.translate(-LABEL_WEST, 0);\r
+\r
+ ypos += cHeight + getAnnotationHeight() + hgap;\r
+\r
+ startRes += cWidth;\r
+ }\r
+\r
+ }\r
+\r
+ AnnotationPanel annotations;\r
+\r
+ int getAnnotationHeight()\r
+ {\r
+ if (!av.isShowAnnotation())\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ return annotations.adjustPanelHeight();\r
+ }\r
+\r
+ private void drawPanel(Graphics g1, int startRes, int endRes,\r
+ int startSeq,\r
+ int endSeq, int offset)\r
+ {\r
+\r
+\r
+ if (!av.hasHiddenColumns())\r
+ {\r
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+ else\r
+ {\r
+\r
+ int screenY = 0;\r
+ int blockStart = startRes;\r
+ int blockEnd = endRes;\r
+\r
+ if (av.hasHiddenColumns())\r
+ {\r
+ for (int[] region : av.getColumnSelection().getHiddenColumns())\r
+ {\r
+ int hideStart = region[0];\r
+ int hideEnd = region[1];\r
+\r
+ if (hideStart <= blockStart)\r
+ {\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
+\r
+ blockEnd = hideStart - 1;\r
+\r
+ g1.translate(screenY * avcharWidth, 0);\r
+\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ if (av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\r
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,\r
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth\r
+ - 1, (endSeq - startSeq) * avcharHeight\r
+ + offset);\r
+ }\r
+\r
+ g1.translate(-screenY * avcharWidth, 0);\r
+ screenY += blockEnd - blockStart + 1;\r
+ blockStart = hideEnd + 1;\r
+ }\r
+ }\r
+ if (screenY <= (endRes - startRes))\r
+ {\r
+ blockEnd = blockStart + (endRes - startRes) - screenY;\r
+ g1.translate(screenY * avcharWidth, 0);\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ g1.translate(-screenY * avcharWidth, 0);\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
+ // int x1, int x2, int y1, int y2, int startx, int starty,\r
+ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,\r
+ int offset)\r
+ {\r
+ g.setFont(av.getFont());\r
+ sr.prepare(g, av.isRenderGaps());\r
+ updateViewport();\r
+ SequenceI nextSeq;\r
+\r
+ // / First draw the sequences\r
+ // ///////////////////////////\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ nextSeq = av.getAlignment().getSequenceAt(i);\r
+\r
+ if (nextSeq == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),\r
+ startRes, endRes, offset + ((i - startSeq) * avcharHeight));\r
+\r
+ if (av.isShowSequenceFeatures())\r
+ {\r
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset\r
+ + ((i - startSeq) * avcharHeight));\r
+ }\r
+\r
+ // / Highlight search Results once all sequences have been drawn\r
+ // ////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
+ endRes);\r
+ if (visibleResults != null)\r
+ {\r
+ for (int r = 0; r < visibleResults.length; r += 2)\r
+ {\r
+ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
+ visibleResults[r + 1], (visibleResults[r] - startRes)\r
+ * avcharWidth, offset\r
+ + ((i - startSeq) * avcharHeight));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.cursorMode && cursorY == i && cursorX >= startRes\r
+ && cursorX <= endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,\r
+ offset + ((i - startSeq) * avcharHeight));\r
+ }\r
+ }\r
+\r
+ if (av.getSelectionGroup() != null\r
+ || av.getAlignment().getGroups().size() > 0)\r
+ {\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+\r
+ }\r
+\r
+ private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,\r
+ int startSeq, int endSeq, int offset)\r
+ {\r
+ //\r
+ // ///////////////////////////////////\r
+ // Now outline any areas if necessary\r
+ // ///////////////////////////////////\r
+ SequenceGroup group = av.getSelectionGroup();\r
+\r
+ int sx = -1;\r
+ int sy = -1;\r
+ int ex = -1;\r
+ int groupIndex = -1;\r
+\r
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))\r
+ {\r
+ group = av.getAlignment().getGroups().get(0);\r
+ groupIndex = 0;\r
+ }\r
+\r
+ if (group != null)\r
+ {\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
+ int alHeight = av.getAlignment().getHeight() - 1;\r
+\r
+ for (i = startSeq; i < endSeq; i++)\r
+ {\r
+ sx = (group.getStartRes() - startRes) * avcharWidth;\r
+ sy = offset + ((i - startSeq) * avcharHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;\r
+\r
+ if (sx + ex < 0 || sx > imgWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ((sx <= (endRes - startRes) * avcharWidth)\r
+ && group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ if ((bottom == -1)\r
+ && (i >= alHeight || !group.getSequences(null)\r
+ .contains(\r
+ av.getAlignment().getSequenceAt(i + 1))))\r
+ {\r
+ bottom = sy + avcharHeight;\r
+ }\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (((top == -1) && (i == 0))\r
+ || !group.getSequences(null).contains(\r
+ av.getAlignment().getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < imgWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ {\r
+ ex = imgWidth;\r
+ }\r
+\r
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * avcharWidth;\r
+ }\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
+\r
+ if (inGroup)\r
+ {\r
+ sy = offset + ((i - startSeq) * avcharHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < imgWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > imgWidth)\r
+ {\r
+ ex = imgWidth;\r
+ }\r
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * avcharWidth;\r
+ }\r
+\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
+\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
+\r
+ inGroup = false;\r
+ }\r
+\r
+ groupIndex++;\r
+\r
+ if (groupIndex >= av.getAlignment().getGroups().size())\r
+ {\r
+ break;\r
+ }\r
+\r
+ group = av.getAlignment().getGroups()\r
+ .get(groupIndex);\r
+ } while (groupIndex < av.getAlignment().getGroups().size());\r
+\r
+ }\r
+ }\r
+\r
+ public void highlightSearchResults(SearchResults results)\r
+ {\r
+ searchResults = results;\r
+\r
+ repaint();\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff