X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=1b4a230a526f78d0d50d6dfe7a7d906372bc5fd0;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=3a4a19751a765381e3260ebf50cbf3dea81b6d5c;hpb=3a45e0d68dde73c005832b7b3924194b214e00ff;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 3a4a197..1b4a230 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 +57,9 @@ 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; /** * Creates a new AnnotationPanel object. @@ -149,74 +149,7 @@ 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 +163,9 @@ 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 +183,9 @@ 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 +200,9 @@ 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 +245,9 @@ 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 +260,6 @@ public class AnnotationPanel extends JPanel implements MouseListener, } adjustPanelHeight(); - activeRes = null; repaint(); return; @@ -363,24 +294,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, } else if(aa[i].graph>0) { - if(SwingUtilities.isRightMouseButton(evt) - && aa[i].graphLines!=null - && aa[i].graphLines.size()>0) - { - SliderPanel sp = new SliderPanel(aa[i], ap); - return; - } - else - { //Stretch Graph graphStretch = i; graphStretchY = evt.getY(); - activeRes = null; - } - } - else - { - activeRes = null; } break; @@ -389,7 +305,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (SwingUtilities.isRightMouseButton(evt)) { - if (activeRes == null) + if (av.getColumnSelection() == null) { return; } @@ -422,40 +338,28 @@ 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(); + } /** @@ -467,6 +371,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { graphStretch = -1; graphStretchY = -1; + mouseDragging = false; } /** @@ -476,6 +381,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseEntered(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(null); } /** @@ -485,8 +392,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseExited(MouseEvent evt) { + if(mouseDragging) + ap.seqPanel.scrollCanvas(evt); } + /** * DOCUMENT ME! * @@ -503,6 +413,56 @@ 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(); + } + + } } /** @@ -539,11 +499,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if ((row > -1) && (res < aa[row].annotations.length) && - (aa[row].annotations[res] != null)) - { - + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + if (row > -1 && res-1) { StringBuffer tip = new StringBuffer(""); @@ -552,15 +512,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null) tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"
" ); } - tip.setLength(tip.length()-4); - this.setToolTipText(tip.toString()+""); + if(tip.length()!=6) + { + tip.setLength(tip.length() - 4); + this.setToolTipText(tip.toString() + ""); + } } - else + else if(aa[row].annotations[res] != null) this.setToolTipText(aa[row].annotations[res].description); - StringBuffer text = new StringBuffer("Sequence position " + - (res + 1) + " " + aa[row].annotations[res].description); - ap.alignFrame.statusBar.setText(text.toString()); + if(aa[row].annotations[res]!=null) + { + StringBuffer text = new StringBuffer("Sequence position " + + (res + 1) + " " + + aa[row].annotations[res].description); + + ap.alignFrame.statusBar.setText(text.toString()); + } } } @@ -622,7 +590,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || + if ((horizontal == 0) || gg==null || (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.getAlignmentAnnotation().length < 1)) { @@ -689,11 +657,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, 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; @@ -710,6 +677,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; + lastSSX = 0; + if (row.graph>0) { @@ -734,10 +704,24 @@ public class AnnotationPanel extends JPanel implements MouseListener, iconOffset = 0; } - for (j = startRes; j < endRes; j++) + int column = startRes; + int yPos = startRes; + + while (yPos < endRes) { - if ((row.annotations.length <= j) || - (row.annotations[j] == null)) + if (av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(yPos); + if (column > row.annotations.length-1) + { + break; + } + } + else + column = yPos; + + if ((row.annotations.length <= column) || + (row.annotations[column] == null)) { validRes = false; } @@ -746,21 +730,21 @@ public class AnnotationPanel extends JPanel implements MouseListener, validRes = true; } - x = (j - startRes) * av.charWidth; + x = (yPos - 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); } } @@ -768,24 +752,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) + (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)))) { - g.drawString(row.annotations[j].displayCharacter, x+charOffset, + g.drawString(row.annotations[column].displayCharacter, x+charOffset, y + iconOffset + 3); } } @@ -793,21 +778,21 @@ 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); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7, 8, 8); break; case 'E': g.setColor(SHEET_COLOUR); - 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 }, new int[] { @@ -820,46 +805,49 @@ 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; } } + + yPos++; } 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.fillRoundRect(lastSSX, y + 4 + iconOffset, + x - lastSSX, 7, 8, 8); break; case 'E': g.setColor(SHEET_COLOUR); - if (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}, new int[] @@ -869,17 +857,15 @@ 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); + g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2); break; } @@ -948,6 +934,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, if(sRes>aa.annotations.length) return; + eRes = Math.min(eRes, aa.annotations.length); + int x = 0; //Adjustment for fastpaint to left @@ -970,38 +958,52 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.setColor(Color.gray); g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2); + eRes = Math.min(eRes, aa.annotations.length); - if(aa.graphLines!=null) + int column = sRes; + int yPos = sRes; + int aaMax = aa.annotations.length-1; + + while( yPos < eRes ) { - for(int l=0; l aaMax) + { + break; + } } - } + else + column = yPos; - eRes = Math.min(eRes, aa.annotations.length); - for (int j = sRes; j < eRes; j++) - { - if(aa.annotations[j]==null || aa.annotations[j-1]==null) + yPos ++; + + if(aa.annotations[column]==null || aa.annotations[column-1]==null) { x+=av.charWidth; 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; } + 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, @@ -1012,48 +1014,50 @@ 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.graphLines!=null) - { - for(int l=0; l aaMax) + { + break; + } + } + else + column = yPos; + + yPos ++; + + if (aa.annotations[column] == null) { x += av.charWidth; 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 ); @@ -1062,7 +1066,19 @@ public class AnnotationPanel extends JPanel implements MouseListener, x += av.charWidth; } + 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