X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=ecd9370f6e1151508177fe5a8b9929223334a599;hb=af2fbc5499bfc4764ad69e1abaa35eee4dd04817;hp=69ae398c406fd127a84ca284ecbf4c82fc7ffbd0;hpb=72f10081ab2cdcd751e5af6af74b8f9305f8a167;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 69ae398..ecd9370 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -24,8 +24,6 @@ import java.awt.*; import java.awt.event.*; import java.awt.image.*; -import java.util.*; - import javax.swing.*; @@ -50,7 +48,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, AlignViewport av; AlignmentPanel ap; int activeRow = -1; - Vector activeRes; BufferedImage image; Graphics2D gg; FontMetrics fm; @@ -60,6 +57,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, //Used For mouse Dragging and resizing graphs int graphStretch = -1; int graphStretchY = -1; + int min; //used by mouseDragged to see if user + int max; //used by mouseDragged to see if user + boolean mouseDragging = false; + + boolean MAC = false; /** * Creates a new AnnotationPanel object. @@ -68,6 +70,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public AnnotationPanel(AlignmentPanel ap) { + + if(System.getProperty("os.name").startsWith("Mac")) + MAC = true; + ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -149,74 +155,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, return height; } - /** - * DOCUMENT ME! - * - * @param col DOCUMENT ME! - */ - public void removeEditableColumn(int col) - { - if (activeRow == -1) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if(aa==null) - return; - - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) - { - activeRow = j; - - break; - } - } - } - - if ((activeRes != null) && activeRes.contains(String.valueOf(col))) - { - activeRes.removeElement(String.valueOf(col)); - } - - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param col DOCUMENT ME! - */ - public void addEditableColumn(int col) - { - if (activeRow == -1) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - if(aa==null) - return; - - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) - { - activeRow = j; - break; - } - } - } - - if (activeRes == null) - { - activeRes = new Vector(); - } - - if (!activeRes.contains(String.valueOf(col))) - { - activeRes.addElement(String.valueOf(col)); - } - - repaint(); - } /** * DOCUMENT ME! @@ -230,10 +169,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (evt.getActionCommand().equals(REMOVE)) { - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - anot[Integer.parseInt(activeRes.get(i).toString())] = null; - anot[Integer.parseInt(activeRes.get(i).toString())] = null; + anot[av.getColumnSelection().columnAt(i)] = null; } } else if (evt.getActionCommand().equals(LABEL)) @@ -251,9 +189,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, aa[activeRow].hasText = true; } - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + int index = av.getColumnSelection().columnAt(i); if (anot[index] == null) { @@ -268,9 +206,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black); - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + int index = av.getColumnSelection().columnAt(i); if (anot[index] == null) { @@ -313,9 +251,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, aa[activeRow].hasText = true; } - for (int i = 0; i < activeRes.size(); i++) + for (int i = 0; i < av.getColumnSelection().size(); i++) { - int index = Integer.parseInt(activeRes.get(i).toString()); + int index = av.getColumnSelection().columnAt(i); if (anot[index] == null) { @@ -328,7 +266,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, } adjustPanelHeight(); - activeRes = null; repaint(); return; @@ -366,11 +303,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, //Stretch Graph graphStretch = i; graphStretchY = evt.getY(); - activeRes = null; - } - else - { - activeRes = null; } break; @@ -379,7 +311,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (SwingUtilities.isRightMouseButton(evt)) { - if (activeRes == null) + if (av.getColumnSelection() == null) { return; } @@ -412,40 +344,28 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if (evt.isControlDown() || evt.isAltDown()) - { - addEditableColumn(res); - } - else if (evt.isShiftDown()) + min = res; + max = res; + + if (av.getColumnSelection().contains(res)) + av.getColumnSelection().removeElement(res); + else { - if (activeRes == null) + av.getColumnSelection().addElement(res); + SequenceGroup sg = new SequenceGroup(); + + for (int i = 0; i < av.alignment.getSequences().size(); i++) { - activeRes = new Vector(); + sg.addSequence(av.alignment.getSequenceAt(i), false); } - else - { - int start = Integer.parseInt(activeRes.get(activeRes.size() - - 1).toString()); - int end = res; - if (end < start) - { - int temp = end; - end = start; - start = temp; - } - - for (int n = start; n <= end; n++) - { - addEditableColumn(n); - } - } - } - else - { - activeRes = new Vector(); - activeRes.addElement(String.valueOf(res)); + sg.setStartRes(res); + sg.setEndRes(res); + av.setSelectionGroup(sg); } + + ap.repaint(); + } /** @@ -457,6 +377,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { graphStretch = -1; graphStretchY = -1; + mouseDragging = false; } /** @@ -466,6 +387,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseEntered(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(null); } /** @@ -475,8 +398,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseExited(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(evt); } + /** * DOCUMENT ME! * @@ -493,6 +419,56 @@ public class AnnotationPanel extends JPanel implements MouseListener, adjustPanelHeight(); ap.repaint(); } + else + { + mouseDragging = true; + + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + + SequenceGroup sg = av.getSelectionGroup(); + + if (res < min) + { + min = res; + } + + if (res > max) + { + max = res; + } + + if (sg != null) + { + if (!av.getColumnSelection().contains(res)) + { + av.getColumnSelection().addElement(res); + } + + if (res > sg.getStartRes()) + { + sg.setEndRes(res); + } + else if (res < sg.getStartRes()) + { + sg.setStartRes(res); + } + + for (int i = min; i <= max; i++) + { + if ((i < sg.getStartRes()) || (i > sg.getEndRes())) + { + av.getColumnSelection().removeElement(i); + } + else + { + av.getColumnSelection().addElement(i); + } + } + + ap.repaint(); + } + + } } /** @@ -529,6 +505,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + if (row > -1 && res-1) @@ -662,6 +641,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void drawComponent(Graphics g, int startRes, int endRes) { + + g.setFont(av.getFont()); if (fm == null) @@ -671,24 +652,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); - if ((av.alignment.getAlignmentAnnotation() == null) || + if ( (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); g.setColor(Color.black); - g.drawString("Alignment has no annotations", 20, 15); + if(av.validCharWidth) + g.drawString("Alignment has no annotations", 20, 15); return; } AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int j; int x = 0; int y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; + char lastSS; + int lastSSX; int iconOffset = av.charHeight / 2; boolean validRes = false; @@ -705,6 +686,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; + lastSSX = 0; if (row.graph>0) @@ -730,10 +713,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, iconOffset = 0; } - for (j = startRes; j < endRes; j++) + int column = startRes; + + while (column < endRes) { - if ((row.annotations.length <= j) || - (row.annotations[j] == null)) + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + if (column > row.annotations.length-1) + { + break; + } + } + + if ((row.annotations.length <= column) || + (row.annotations[column] == null)) { validRes = false; } @@ -742,46 +736,50 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (j - startRes) * av.charWidth; + x = (column - startRes) * av.charWidth; if (activeRow == i) { g.setColor(Color.red); - if (activeRes != null) + if (av.getColumnSelection() != null) { - for (int n = 0; n < activeRes.size(); n++) + for (int n = 0; n < av.getColumnSelection().size(); n++) { - int v = Integer.parseInt(activeRes.get(n).toString()); + int v = av.getColumnSelection().columnAt(n); - if (v == j) + if (v == column) { - g.fillRect((j - startRes) * av.charWidth, y, + g.fillRect((column - startRes) * av.charWidth, y, av.charWidth, row.height); } } } } - if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) + if (av.validCharWidth && validRes && + (row.annotations[column].displayCharacter.length() > 0)) { int charOffset = (av.charWidth - - fm.charWidth(row.annotations[j].displayCharacter.charAt( + fm.charWidth(row.annotations[column].displayCharacter.charAt( 0))) / 2; - g.setColor(row.annotations[j].colour); + g.setColor(row.annotations[column].colour); - if (j == 0 || row.graph>0) + if (column == 0 || row.graph>0) { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, + g.drawString(row.annotations[column].displayCharacter, x+charOffset, y + iconOffset + 3); } - else if (((row.annotations[j - 1] == null) || - (row.annotations[j].displayCharacter != row.annotations[j - - 1].displayCharacter))) + else if ( + row.annotations[column - 1] == null + ||(!row.annotations[column].displayCharacter.equals( + row.annotations[column - 1].displayCharacter) + || + (row.annotations[column].displayCharacter.length() <2 && + row.annotations[column].secondaryStructure==' '))) { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, + g.drawString(row.annotations[column].displayCharacter, x+charOffset, y + iconOffset + 3); } } @@ -789,26 +787,52 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (row.hasIcons) { if (!validRes || - (row.annotations[j].secondaryStructure != lastSS[i])) + (row.annotations[column].secondaryStructure != lastSS)) { - switch (lastSS[i]) + switch (lastSS) { case 'H': g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); + if(MAC) + { + //Off by 1 offset when drawing rects and ovals + //to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7, 8, 8); + break; + } + + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = x; + + if(sCol==0 || + row.annotations[sCol-1]==null || + row.annotations[sCol-1].secondaryStructure!='H') + { + g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ; + x1 += av.charWidth/2; + } + + if(row.annotations[column]==null || + row.annotations[column].secondaryStructure!='H') + { + g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180); + x2 -= av.charWidth/2; + } + g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7); break; case 'E': g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] { x - 4, x - 4, x }, + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX - 4, 7); + g.fillPolygon(new int[] { x - 5, x - 5, x }, new int[] { y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset + y + 7 + iconOffset }, 3); break; @@ -816,49 +840,79 @@ public class AnnotationPanel extends JPanel implements MouseListener, default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, - x - lastSSX[i], 2); + g.fillRect(lastSSX, y + 6 + iconOffset, + x - lastSSX, 2); break; } if (validRes) { - lastSS[i] = row.annotations[j].secondaryStructure; + lastSS = row.annotations[column].secondaryStructure; } else { - lastSS[i] = ' '; + lastSS = ' '; } - lastSSX[i] = x; + lastSSX = x; } } + + column++; } x += av.charWidth; if (row.hasIcons) { - switch (lastSS[i]) + switch (lastSS) { case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); + g.setColor(HELIX_COLOUR); + if (MAC) + { + //Off by 1 offset when drawing rects and ovals + //to offscreen image on the MAC + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7, 8, 8); + break; + } + + + int sCol = (lastSSX / av.charWidth) + startRes; + int x1 = lastSSX; + int x2 = x; + + if(sCol==0 || + row.annotations[sCol-1]==null || + row.annotations[sCol-1].secondaryStructure!='H') + { + g.fillArc(lastSSX, y+4+iconOffset, av.charWidth+1, 7, 90,180) ; + x1 += av.charWidth/2; + } + + if(row.annotations[column]==null || + row.annotations[column].secondaryStructure!='H') + { + g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 7, 270,180); + x2 -= av.charWidth/2; + } + + g.fillRect(x1, y+4+iconOffset, x2-x1+1, 7); break; case 'E': g.setColor(SHEET_COLOUR); - if (row.annotations[endRes] !=null - && row.annotations[endRes].secondaryStructure != 'E') + if (row.annotations[endRes] ==null + || row.annotations[endRes].secondaryStructure != 'E') { - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX - 4, 7); g.fillPolygon(new int[] - {x - 4, x - 4, x}, + {x - 5, x - 5, x}, new int[] { y + iconOffset, y + 14 + iconOffset, @@ -866,17 +920,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, }, 3); } else - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7); + g.fillRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7); break; - case 'C': - break; default: g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2); + if(!av.wrapAlignment || endRes==av.endRes) + g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2); break; } @@ -945,12 +998,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; + int x = 0; //Adjustment for fastpaint to left if(eRes aaMax) + { + break; + } + } + + if(aa.annotations[column]==null || aa.annotations[column-1]==null) { x+=av.charWidth; + column ++; continue; } - g.setColor(aa.annotations[j].colour); - y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight); - y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight); + + + g.setColor(aa.annotations[column].colour); + y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight); + y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight); + g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2); x += av.charWidth; + + column++; + } + if(aa.threshold!=null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + + y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); + } } public void drawBarGraph(Graphics g, AlignmentAnnotation aa, @@ -1006,47 +1080,45 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; + eRes = Math.min(eRes, aa.annotations.length); + int x=0, y1, y2; float range = max - min; - if(aa.threshold!=null) - { - g.setColor(aa.threshold.colour); - Graphics2D g2 = (Graphics2D)g; - g2.setStroke(new BasicStroke(1, - BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, - new float[] { 5f, 3f }, 0f)); - - y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); - g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2); - g2.setStroke(new BasicStroke()); - } - y1 = y2 = y; if(min<0) - y2 = (int)(y - (0-min / (range))*aa.graphHeight); + y2 = y - (int)((0-min / (range))*aa.graphHeight); g.setColor(Color.gray); - g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2); + g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2); - eRes = Math.min(eRes, aa.annotations.length-1); + int column = sRes; + int aaMax = aa.annotations.length-1; - for (int j = sRes; j < eRes; j++) + while( column < eRes ) { + if(av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + if(column > aaMax) + { + break; + } + } - if (aa.annotations[j] == null) + if (aa.annotations[column] == null) { x += av.charWidth; + column ++; continue; } - g.setColor(aa.annotations[j].colour); - y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight); + g.setColor(aa.annotations[column].colour); + y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight); if(y1-y2>0) g.fillRect(x, y2, av.charWidth, y1-y2 ); @@ -1054,8 +1126,22 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.fillRect(x, y1, av.charWidth, y2-y1 ); x += av.charWidth; + column ++; + } + if(aa.threshold!=null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); + } } // used by overview window