import java.awt.*;
import java.awt.event.*;
+import java.util.Hashtable;
+import java.util.Vector;
import jalview.datamodel.*;
idPanel = new IdPanel(av, this);
scalePanel = new ScalePanel(av, this);
idwidthAdjuster = new IdwidthAdjuster(this);
+// annotationScroller = new ScrollPane();
+ // annotationScroller.setBackground(Color.white);
annotationPanel = new AnnotationPanel(this);
-
- sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
+ annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
+ // annotationScroller.setPreferredSize(new Dimension(10,80));
+// annotationScroller.add(annotationPanel);
+// annotationScroller.getInsets().set(0,0,0,0);
+
+ sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
alabels = new AnnotationLabels(this);
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
+
fontChanged();
setScrollValues(0, 0);
+ apvscroll.addAdjustmentListener(this);
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
annotationSpaceFillerHolder.setSize(d.width,
annotationPanel.getSize().height);
alabels.setSize(d.width, annotationPanel.getSize().height);
-
final AlignmentPanel ap = this;
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
- int ap = annotationPanel.adjustPanelHeight();
+ int ap = annotationPanel.adjustPanelHeight(false);
annotationPanel.repaint();
Dimension d = calculateIdWidth();
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
+ if (evt == null || evt.getSource()==apvscroll)
+ {
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ //annotationPanel.image=null;
+ //alabels.image=null;
+ //alabels.repaint();
+ //annotationPanel.repaint();
+ }
if (evt == null || evt.getSource() == hscroll)
{
int x = hscroll.getValue();
invalidate();
Dimension d = idPanel.idCanvas.getSize();
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ annotationPanelHolder.setSize(seqPanel.getSize().width, annotationPanel.getSize().height);
annotationSpaceFillerHolder.setSize(d.width,
annotationPanel.getSize().height);
- alabels.setSize(d.width, annotationPanel.getSize().height);
+ alabels.setSize(d.width, annotationPanelHolder.getSize().height);
if (av.getWrapAlignment())
{
if (canvasWidth > 0)
{
int max = maxwidth / canvasWidth;
- vscroll.setMaximum(max);
+ vscroll.setMaximum(1+max);
vscroll.setUnitIncrement(1);
vscroll.setVisibleAmount(1);
}
BorderLayout borderLayout2 = new BorderLayout();
+ Panel annotationPanelHolder = new Panel();
+ protected Scrollbar apvscroll=new Scrollbar();
+
+ BorderLayout borderLayout12 = new BorderLayout();
+
private void jbInit() throws Exception
{
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
hscroll.setOrientation(Scrollbar.HORIZONTAL);
hscrollHolder.setLayout(borderLayout10);
hscrollFillerPanel.setBackground(Color.white);
+ apvscroll.setOrientation(Scrollbar.VERTICAL);
+ apvscroll.setVisible(true);
+ apvscroll.addAdjustmentListener(this);
+ annotationPanelHolder.setBackground(Color.white);
+ annotationPanelHolder.setLayout(borderLayout12);
+ annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
// hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
hscrollHolder.setBackground(Color.white);
this.add(sequenceHolderPanel, BorderLayout.CENTER);
}
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
+ boolean updateCalcs = false;
+ boolean conv = av.isShowGroupConservation();
+ boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
+ /**
+ * automatically adjust annotation panel height for new annotation
+ * whilst ensuring the alignment is still visible.
+ */
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getHeight() == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ fontChanged();
+ int height = annotationPanel.adjustPanelHeight();
+ if (hscroll.isVisible())
+ {
+ height += hscroll.getPreferredSize().height;
+ }
+ int mheight=height;
+ // sets initial preferred height
+ if (height > alignFrame.getHeight() / 2)
+ {
+ height = alignFrame.getHeight() / 2;
+ }
+ apvscroll.setValues(apvscroll.getValue(), height, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ apvscroll.addNotify();
+ hscroll.addNotify();
+
+ annotationPanelHolder.setPreferredSize(new Dimension(annotationPanel
+ .getWidth(), height));
+
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ annotationSpaceFillerHolder.getWidth(), height));
+
+ //annotationScroller.validate();// repaint();
+ validate();
+ addNotify();
+ repaint();
+ }
+
}
import java.awt.*;
import java.awt.event.*;
+import java.awt.image.BufferedImage;
import jalview.datamodel.*;
this.ap = ap;
this.av = ap.av;
setLayout(null);
+
+ java.net.URL url = getClass().getResource("/images/idwidth.gif");
+ Image temp = null;
+
+ if (url != null)
+ {
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+ }
+
+ try
+ {
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(temp, 0);
+ mt.waitForID(0);
+ } catch (Exception ex)
+ {
+ }
+
+ BufferedImage bi = new BufferedImage(temp.getHeight(this),
+ temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
+ Graphics2D g = (Graphics2D) bi.getGraphics();
+ g.rotate(Math.toRadians(90));
+ g.drawImage(temp, 0, -bi.getWidth(this), this);
+ image = (Image) bi;
+
addMouseListener(this);
addMouseMotionListener(this);
}
}
+ boolean resizePanel = false;
+
public void mouseMoved(MouseEvent evt)
{
- int row = getSelectedRow(evt.getY() - scrollOffset);
+ resizePanel = evt.getY() < 10;
+
+ int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
{
}
+ MouseEvent dragEvent = null;
+
public void mouseDragged(MouseEvent evt)
{
+ dragEvent = evt;
+
+ if (resizePanel)
+ {
+ Dimension d = ap.annotationPanelHolder.getSize(),e = ap.annotationSpaceFillerHolder.getSize();;
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.charHeight;
+ dif *= ap.av.charHeight;
+
+ if ((d.height - dif) > 20)
+ {
+
+ setPreferredSize(new Dimension(e.width,d.height-dif));
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(e.width, d.height - dif));
+ ap.annotationPanelHolder.setPreferredSize(new Dimension(d.width, d.height - dif));
+ ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height-dif, 0, ap.annotationPanel.adjustPanelHeight(false));
+
+ ap.validate();
+ //ap.paintAlignment(true);
+ }
+
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
}
public void mouseClicked(MouseEvent evt)
public void mouseReleased(MouseEvent evt)
{
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.annotationPanel.repaint();
}
public void mouseEntered(MouseEvent evt)
{
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
}
public void mouseExited(MouseEvent evt)
{
+
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ }
+ else
+ {
+ if (!resizePanel)
+ {
+ dragEvent = null;
+ }
+ }
+ repaint();
}
public void mousePressed(MouseEvent evt)
{
- selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+ oldY = evt.getY();
+ // todo: move below to mouseClicked ?
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);
+
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
+ PopupMenu popup = new PopupMenu("Annotations");
- PopupMenu popup = new PopupMenu("Annotations");
-
- MenuItem item = new MenuItem(ADDNEW);
- item.addActionListener(this);
- popup.add(item);
- if (selectedRow < 0)
- {
- // this never happens at moment: - see comment on JAL-563
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < 0)
+ {
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ // add the rest if there are actually rows to show
+ item = new MenuItem(EDITNAME);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(HIDE);
+ item.addActionListener(this);
+ popup.add(item);
if (hasHiddenRows)
{
item = new MenuItem(SHOWALL);
popup.add(item);
}
this.add(popup);
- popup.show(this, evt.getX(), evt.getY());
- return;
- }
- // add the rest if there are actually rows to show
- item = new MenuItem(EDITNAME);
- item.addActionListener(this);
- popup.add(item);
- item = new MenuItem(HIDE);
- item.addActionListener(this);
- popup.add(item);
- if (hasHiddenRows)
- {
- item = new MenuItem(SHOWALL);
+ item = new MenuItem(OUTPUT_TEXT);
item.addActionListener(this);
popup.add(item);
- }
- this.add(popup);
- item = new MenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- popup.add(item);
- if (aa[selectedRow] == ap.av.consensus)
- {
- popup.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
-
- cbmi.addItemListener(new ItemListener()
+ if (aa[selectedRow] == ap.av.consensus)
{
- public void itemStateChanged(ItemEvent e)
+ popup.addSeparator();
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+ "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
+
+ cbmi.addItemListener(new ItemListener()
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.paintAlignment(true);
- }
- });
- popup.add(cbmi);
- item = new MenuItem(COPYCONS_SEQ);
- item.addActionListener(this);
- popup.add(item);
- }
+ public void itemStateChanged(ItemEvent e)
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ ap.paintAlignment(true);
+ }
+ });
+ popup.add(cbmi);
+ item = new MenuItem(COPYCONS_SEQ);
+ item.addActionListener(this);
+ popup.add(item);
+ }
- popup.show(this, evt.getX(), evt.getY());
- } else {
+ popup.show(this, evt.getX(), evt.getY());
+ }
+ else
+ {
// selection action.
if (selectedRow > -1 && selectedRow < aa.length)
{
{
if (evt.getClickCount() >= 2)
{
- // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+ // todo: make the ap scroll to the selection - not necessary, first
+ // click highlights/scrolls, second selects
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
ap.av.setSelectionGroup(// new SequenceGroup(
aa[selectedRow].groupRef); // );
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
- g.translate(0, scrollOffset);
+ g.translate(0, -scrollOffset);
g.setColor(Color.black);
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
g.drawString(aa[i].label, x, y + offset);
}
}
+ g.translate(0, +scrollOffset);
+ if (resizePanel)
+ {
+ g.setColor(Color.red);
+ g.setPaintMode();
+ g.drawLine(2, 8, 5, 2);
+ g.drawLine(5, 2, 8, 8);
+ }
+ else if (dragEvent != null && aa != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY());
+ }
+
+ if ((aa == null) || (aa.length < 1))
+ {
+ g.setColor(Color.black);
+ g.drawString("Right click", 2, 8);
+ g.drawString("to add annotation", 2, 18);
+ }
}
}
import java.awt.*;
import java.awt.event.*;
+import java.awt.font.LineMetrics;
+import java.awt.geom.AffineTransform;
+
+import jalview.analysis.AAFrequency;
import jalview.datamodel.*;
import jalview.schemes.ColourSchemeI;
this.ap = ap;
av = ap.av;
setLayout(null);
- adjustPanelHeight();
+ int height = adjustPanelHeight();
+ ap.apvscroll.setValues(0, getHeight(), 0, height);
addMouseMotionListener(this);
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset(-evt.getValue());
}
/**
return;
}
- int height = 0;
+ int height = -scrollOffset;
activeRow = -1;
for (int i = 0; i < aa.length; i++)
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
public int adjustPanelHeight()
{
+ return adjustPanelHeight(true);
+ }
+
+ public int adjustPanelHeight(boolean repaint)
+ {
+
// setHeight of panels
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int height = 0;
{
height = 20;
}
- this.setSize(getSize().width, height);
- repaint();
+ this.setPreferredSize(new Dimension(getSize().width, height));
+ if (repaint)
+ {
+ repaint();
+ }
return height;
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
+ g.translate(0, -scrollOffset);
int x = 0;
int y = 0;
int column = 0;
y += aa[i].height;
}
}
+ g.translate(0, +scrollOffset);
}
public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
int column;
int aaMax = aa.annotations.length - 1;
boolean renderHistogram = true, renderProfile = false;
- /*
- * Logos are disabled for 2.5 release : Bug # 0060064 if (aa.autoCalculated
- * && aa.label.startsWith("Consensus")) { // TODO: generalise this to have
- * render styles for consensus/profile data if (aa.groupRef!=null) {
- * renderHistogram = aa.groupRef.isShowConsensusHistogram(); renderProfile =
- * aa.groupRef.isShowSequenceLogo(); } else { renderHistogram =
- * av.isShowConsensusHistogram(); renderProfile = av.isShowSequenceLogo(); }
- * }
- */
+ if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ { // TODO: generalise this to have render styles for consensus/profile data
+ if (aa.groupRef != null)
+ {
+ renderHistogram = aa.groupRef.isShowConsensusHistogram();
+ renderProfile = aa.groupRef.isShowSequenceLogo();
+ }
+ else
+ {
+ renderHistogram = av.isShowConsensusHistogram();
+ renderProfile = av.isShowSequenceLogo();
+ }
+ }
+
while (x < eRes - sRes)
{
column = sRes + x;
}
}
// draw profile if available
- // Disabled for 2.5 release: see bug #0060064
- /**
- * if (aa.annotations[column].value!=0 && renderProfile) { int profl[] =
- * getProfileFor(aa,column); int ht = y1; //,htn=y2-y1;//aa.graphHeight;
- * float wdth; double ht2=0; char[] dc = new char[1]; // LineMetrics lm;
- * for (int c=1;profl!=null && c<profl[0];) { dc[0] = (char) profl[c++];
- * wdth = av.charWidth; wdth/=(float) fm .charsWidth(dc,0,1);
- *
- * if (c>2) { ht+=(int)ht2; } { // not java 1.1 compatible: Bug # 0060064
- * g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
- * (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight))); lm =
- * g.getFontMetrics().getLineMetrics(dc,0,1, g);
- * g.setColor(profcolour.findColour(dc[0]));
- * g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight())); } }
- * g.setFont(ofont); }
- **/
+ if (aa.annotations[column].value != 0 && renderProfile)
+ {
+ int profl[] = getProfileFor(aa, column);
+ int ht = y1, htn = y2 - y1;// aa.graphHeight;
+ float wdth;
+ double ht2 = 0;
+ char[] dc = new char[1];
+ LineMetrics lm;
+ for (int c = 1; profl != null && c < profl[0];)
+ {
+ dc[0] = (char) profl[c++];
+ wdth = av.charWidth;
+ wdth /= (float) fm.charsWidth(dc, 0, 1);
+
+ if (c > 2)
+ {
+ ht += (int) ht2;
+ }
+ { // not java 1.1 compatible: Bug # 0060064
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
+ / av.charHeight)));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+ g.setColor(profcolour.findColour(dc[0]));
+ g.drawChars(dc, 0, 1, x * av.charWidth,
+ (int) (ht + lm.getHeight()));
+ }
+ }
+ g.setFont(ofont);
+ }
+
x++;
}
}
}
- /*
- * Disabled for 2.5 release - see bug #0060064 private int[]
- * getProfileFor(AlignmentAnnotation aa, int column) { // if
- * (aa.autoCalculated && aa.label.startsWith("Consensus")) { if
- * (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // &&
- * aa.groupRef.isShowSequenceLogo()) { return
- * AAFrequency.extractProfile(aa.groupRef
- * .consensusData[column],aa.groupRef.getIgnoreGapsConsensus()); } // TODO
- * extend annotation row to enable dynamic and static profile data to be
- * stored if (aa.groupRef==null && aa.sequenceRef==null) // &&
- * av.isShowSequenceLogo()) { return
- * AAFrequency.extractProfile(av.hconsensus[column
- * ],av.getIgnoreGapsConsensus()); } // } return null; }
- */
+ private int[] getProfileFor(AlignmentAnnotation aa, int column)
+ {
+ // if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
+ if (aa.groupRef != null && aa.groupRef.consensusData != null)
+ {
+ // && aa.groupRef.isShowSequenceLogo()) {
+ return AAFrequency.extractProfile(aa.groupRef.consensusData[column],
+ aa.groupRef.getIgnoreGapsConsensus());
+ }
+ // TODO extend annotation row to enable dynamic and static profile data to
+ // be stored
+ if (aa.groupRef == null && aa.sequenceRef == null)
+ // && av.isShowSequenceLogo())
+ {
+ return AAFrequency.extractProfile(av.hconsensus[column],
+ av.getIgnoreGapsConsensus());
+ }
+ // }
+ return null;
+ }
// used by overview window
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
x += av.charWidth;
}
}
+
+ int scrollOffset = 0;
+
+ public void setScrollOffset(int value)
+ {
+ scrollOffset = value;
+ repaint();
+ }
}
git://source.jalview.org / jalview.git / commitdiff