--- /dev/null
+build
+buildPropertiesFile
+buildTests
+buildextclients
+buildindices
+castorbinding
+clean
+compileApplet
+distclean
+help
+init
+linkcheck
+makeApplet
+makedist
+makefulldist
+obfuscate
+packageApplet
+prepare
+prepareTests
+preparejnlp
+prepubapplet_1
+pubapplet
+runenv
+signApplet
+sourcedist
+sourcedoc
+sourcescrub
+testclean
+testng
+usage
+writejnlpf
<mapID target="printSetupIcon" url="icons/setup.png" />
<mapID target="overview" url="html/features/overview.html" />
+ <mapID target="overviewprefs" url="html/features/preferences.html#overview" />
</map>
<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
<tocitem text="Custom Colourschemes in Groovy" target="groovy.colours"/>
<tocitem text="Omit hidden regions in Overview" target="overview"/>
+ <tocitem text="Show gaps as grey in overview" target="overviewprefs"/>
<tocitem text="identifers.org for URL Links" target="linksprefs" />
<tocitem text="New features in Split Frame View" target="splitframe.mirrorfonts" />
</tocitem>
<strong>View→Overview window</strong>
</p>
<p>Select the overview window menu item to get a navigable image
- of the whole alignment.</p>
+ of the whole alignment. By default, gaps are shown as dark grey, in
+ the overview (since 2.10.2b1).</p>
<p>The red box indicates the currently viewed region of the
alignment, this may be moved by clicking and dragging with the
mouse.</p>
<p>Click anywhere else in the overview to centre the view on that
position</p>
- <p></p>
+ <p></p>
<p>
<strong>Hiding hidden regions in the overview</strong>
</p>
Hidden sequences and columns are by default shown as dark-grey rows
and columns in the overview. Hidden regions can also be omitted
entirely (to make the Overview 'WYSIWIG') by <strong>Right-clicking</strong>
- (or CMD-Clicking) to open the overview's popup menu.<br />
- <br /> <em>The option to include/exclude hidden regions in the
+ (or CMD-Clicking) to open the overview's popup menu.<br /> <br />
+ <em>The option to include/exclude hidden regions in the
overview was introduced in Jalview 2.10.2</em>.
<p>
<img src="overview.gif" width="407" height="137">
</p>
<p> </p>
+ <em>Previous to 2.10.2b1, gaps were white, and sequences shown as
+ dark grey unless coloured.</em>
</body>
</html>
Preferences</a> tab allows you to configure default colourschemes
for a new alignment window.
</li>
+ <li>The <a href="#overview"><strong>"Overview"</strong>
+ Preferences</a> tab configures defaults for the overview window.
+ </li>
<li>The <a href="#structure"><strong>"Structure"</strong>
Preferences</a> tab allows you to configure options for obtaining
and displaying structure information.
by Annotation...</a> is selected from the alignment window's colours
menu.
</p>
+ <p>
+ <a name="overview"><strong>"Overview"
+ Preferences tab</strong>
+ </p>
+ <p>
+ <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
+ Jalview's overview shows gaps as white, and sequences with no
+ colourscheme applied as grey.
+ </p>
+ <p>
+ <em>Show Hidden regions when opening overview</em> - default setting
+ for inclusion of hidden regions.
+ </p>
+ <p>
+ <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
+ configures the default colour for gaps in the overview.
+ </p>
+ <p>
+ <em>Hidden Colour</em> - colour used to highlight regions in the
+ overview that are hidden in the alignment.
+ </p>
+ <p>
+ <em>Gap Colour</em> - The default colour scheme for a new alignment
+ window. If the chosen option is "User Defined" then the
+ last User Defined Colour loaded or saved via the User Defined
+ Colours panel will be loaded.
+ </p>
<p>
<a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
<td><div align="left">
<em></em>
<ul>
+ <li>
+ <!-- JAL-2588 -->Show gaps in overview window by colouring
+ in grey (sequences used to be coloured grey, and gaps were
+ white)
+ </li>
+ <li><!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop Preferences</li>
</ul>
</div></td>
<td><div align="left">
<em></em>
<ul>
+ <li>
+ <!-- JAL-2664 -->Overview window redraws every hidden
+ column region row by row
+ </li>
+ <li>
+ <!-- JAL-2681 -->duplicate protein sequences shown after
+ retrieving Ensembl crossrefs for sequences from Uniprot
+ </li>
+ <li>
+ <!-- JAL-2603 -->Overview window throws NPE if show boxes
+ format setting is unticked
+ </li>
+ <li>
+ <!-- JAL-2610 -->Groups are coloured wrongly in overview
+ if group has show boxes format setting unticked
+ </li>
+ <li>
+ <!-- JAL-2672,JAL-2665 -->Redraw problems when autoscrolling whilst
+ dragging current selection group to include sequences and
+ columns not currently displayed
+ </li>
</ul>
</div></td>
This is patch release for 2.10.2. See the <a
href="releases.html#Jalview.2.10.2b1">release notes</a>.
</p>
+ <ul>
+ <li>Gaps are now rendered as dark grey in overview window</li>
+ </ul>
<p>
<strong>What's new in Jalview 2.10.2 ?</strong>
</p>
label.show_experimental = Enable experimental features
label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
label.warning_hidden = Warning: {0} {1} is currently hidden
+label.overview_settings = Overview settings
+label.ov_legacy_gap = Use legacy gap colouring (gaps are white)
+label.gap_colour = Gap colour:
+label.ov_show_hide_default = Show hidden regions when opening overview
+label.hidden_colour = Hidden colour:
+label.select_gap_colour = Select gap colour
+label.select_hidden_colour = Select hidden colour
+label.overview = Overview
+label.reset_to_defaults = Reset to defaults
\ No newline at end of file
label.show_experimental = Habilitar funciones experimentales
label.show_experimental_tip = Habilitar funciones nuevas y experimentales (ver Latest Release Notes para más detalles)
label.warning_hidden = Advertencia: {0} {1} está actualmente oculto
+label.overview_settings = Ajustes para la ventana resumen
+label.ov_legacy_gap = <html>Utilizar el color heredado de huecos<br>(los huecos son blancos)
+label.gap_colour = Color de huecos:
+label.ov_show_hide_default = Mostrar regiones ocultas al abrir el resumen
+label.hidden_colour = Color de las regiones ocultas:
+label.select_gap_colour = Seleccionar color de huecos
+label.select_hidden_colour = Seleccionar color de las regiones ocultas
+label.overview = Resumen
+label.reset_to_defaults = Restablecen a los predeterminados
\ No newline at end of file
* @return true if the column at the position is hidden
*/
public boolean isHidden(int c);
+
+ /**
+ * Answers if any column in this collection is hidden
+ *
+ * @return true if there is at least 1 hidden column
+ */
+ public boolean hasHidden();
}
public boolean isHidden(int r);
/**
+ * Answers if any row in this collection is hidden
+ *
+ * @return true if there is at least 1 hidden row
+ */
+ public boolean hasHidden();
+
+ /**
* Answers the sequence at the given position in the alignment
*
* @param r
package jalview.appletgui;
import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
private AlignViewport av;
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
private jalview.renderer.seqfeatures.FeatureRenderer fr;
private Frame nullFrame;
nullFrame = new Frame();
nullFrame.addNotify();
- sr = new SequenceRenderer(av);
- sr.graphics = nullFrame.getGraphics();
- sr.renderGaps = false;
- sr.forOverview = true;
fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
}
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
- or = new OverviewRenderer(sr, fr, od);
+ or = new OverviewRenderer(fr, od, av.getAlignment(),
+ av.getResidueShading(), new OverviewResColourFinder());
miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
+import jalview.renderer.ResidueColourFinder;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import java.awt.Color;
boolean renderGaps = true;
- SequenceGroup currentSequenceGroup = null;
-
SequenceGroup[] allGroups = null;
Color resBoxColour;
Graphics graphics;
- boolean forOverview = false;
+ ResidueColourFinder resColourFinder;
public SequenceRenderer(AlignViewport av)
{
this.av = av;
+ resColourFinder = new ResidueColourFinder();
}
/**
this.renderGaps = renderGaps;
}
- protected Color getResidueBoxColour(SequenceI seq, int i)
- {
- allGroups = av.getAlignment().findAllGroups(seq);
-
- if (inCurrentSequenceGroup(i))
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.getResidueShading(), seq, i);
- }
-
- return resBoxColour;
- }
-
/**
* Get the residue colour at the given sequence position - as determined by
* the sequence group colour (if any), else the colour scheme, possibly
{
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
- Color col = getResidueBoxColour(seq, position);
-
- if (finder != null)
- {
- col = finder.findFeatureColour(col, seq, position);
- }
- return col;
- }
-
- void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
- {
- if (shader.getColourScheme() != null)
- {
- resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
- }
- else if (forOverview
- && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
- {
- resBoxColour = Color.lightGray;
- }
- else
- {
- resBoxColour = Color.white;
- }
-
+ return resColourFinder.getResidueColour(av.getShowBoxes(),
+ av.getResidueShading(),
+ allGroups, seq, position, finder);
}
public Color findSequenceColour(SequenceI seq, int i)
int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
avCharHeight = av.getCharHeight();
+ Color resBoxColour = Color.white;
Color tempColour = null;
while (i <= end)
{
resBoxColour = Color.white;
if (i < length)
{
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
}
continue;
}
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
if (currentSequenceGroup.getColourText())
{
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
graphics.setColor(resBoxColour.darker());
}
if (currentSequenceGroup.getShowNonconserved())
if (av.getColourText())
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
graphics.setColor(resBoxColour.darker());
return sequenceChar;
}
- boolean inCurrentSequenceGroup(int res)
- {
- if (allGroups == null)
- {
- return false;
- }
-
- for (int i = 0; i < allGroups.length; i++)
- {
- if (allGroups[i].getStartRes() <= res
- && allGroups[i].getEndRes() >= res)
- {
- currentSequenceGroup = allGroups[i];
- return true;
- }
- }
-
- return false;
- }
-
- public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
- int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end,
+ int x1, int y1)
{
int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
int pady = avCharHeight / 5;
{
return !hidden.isVisible(c);
}
+
+ @Override
+ public boolean hasHidden()
+ {
+ return hidden.hasHiddenColumns();
+ }
}
{
return alignment.getSequenceAtAbsoluteIndex(seq);
}
+
+ @Override
+ public boolean hasHidden()
+ {
+ return (hidden.getSize() > 0);
+ }
}
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
*/
public class SequenceGroup implements AnnotatedCollectionI
{
+ // TODO ideally this event notification functionality should be separated into
+ // a
+ // subclass of ViewportProperties similarly to ViewportRanges. Done here as
+ // quick fix for JAL-2665
+ public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+ protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
+ public void addPropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ public void removePropertyChangeListener(PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+ // end of event notification functionality initialisation
+
String groupName;
String description;
if (s != null && !sequences.contains(s))
{
sequences.add(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() - 1, sequences.size());
}
if (recalc)
synchronized (sequences)
{
sequences.remove(s);
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+ sequences.size() + 1, sequences.size());
if (recalc)
{
*/
public void setStartRes(int i)
{
+ int before = startRes;
startRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
}
/**
*/
public void setEndRes(int i)
{
+ int before = endRes;
endRes = i;
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
}
/**
{
synchronized (sequences)
{
+ int before = sequences.size();
sequences.clear();
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+ sequences.size());
}
}
return false;
}
+ @Override
+ public boolean hasHidden()
+ {
+ return false;
+ }
+
}
{
return alignment.getSequenceAtAbsoluteIndex(seq);
}
+
+ @Override
+ public boolean hasHidden()
+ {
+ return false;
+ }
}
String translation = null;
String proteinName = "";
String proteinId = null;
- Map<String, String> vals = new Hashtable<String, String>();
+ Map<String, String> vals = new Hashtable<>();
/*
* codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
* single graphics context), then reset to (0, scale height)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
- getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
- startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq);
alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
if (av.isShowAnnotation() && (endSeq == alignmentHeight))
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
totalHeight, 0);
if ((pi * pheight) < totalHeight)
package jalview.gui;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
private AlignViewportI av;
+ private OverviewResColourFinder cf;
+
public OverviewCanvas(OverviewDimensions overviewDims,
AlignViewportI alignvp)
{
sr = new SequenceRenderer(av);
sr.renderGaps = false;
- sr.forOverview = true;
fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+
+ boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+ Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+ Preferences.OVERVIEW_DEFAULT_GAP);
+ Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+ Preferences.OVERVIEW_DEFAULT_HIDDEN);
+ cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
}
/**
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
- or = new OverviewRenderer(sr, fr, od);
+ or = new OverviewRenderer(fr, od, av.getAlignment(),
+ av.getResidueShading(), cf);
miniMe = or.draw(od.getRows(av.getAlignment()),
od.getColumns(av.getAlignment()));
*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.OverviewDimensions;
this.av = alPanel.av;
this.ap = alPanel;
- od = new OverviewDimensionsShowHidden(av.getRanges(),
+ showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ true);
+ if (showHidden)
+ {
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
(av.isShowAnnotation()
&& av.getAlignmentConservationAnnotation() != null));
+ }
+ else
+ {
+ od = new OverviewDimensionsHideHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
+ }
setSize(od.getWidth(), od.getHeight());
}
}
else
- // if (!av.getWrapAlignment())
{
if (!od.isPositionInBox(evt.getX(), evt.getY()))
{
public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
+ public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+ public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+ public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+ .darker();
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
* .properties file as '|' separated strings
*/
- groupURLLinks = new ArrayList<String>();
+ groupURLLinks = new ArrayList<>();
}
JInternalFrame frame;
Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
/*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR, OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+
+ /*
* Set Structure tab defaults.
*/
final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
maxColour.getBackground());
/*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*
* Save Structure settings
*/
Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
}
@Override
+ public void gapColour_actionPerformed(JPanel gap)
+ {
+ if (!useLegacyGap.isSelected())
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_gap_colour"),
+ gapColour.getBackground());
+ if (col != null)
+ {
+ gap.setBackground(col);
+ }
+ gap.repaint();
+ }
+ }
+
+ @Override
+ public void hiddenColour_actionPerformed(JPanel hidden)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_hidden_colour"),
+ hiddenColour.getBackground());
+ if (col != null)
+ {
+ hidden.setBackground(col);
+ }
+ hidden.repaint();
+ }
+
+ @Override
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ boolean enabled = useLegacyGap.isSelected();
+ if (enabled)
+ {
+ gapColour.setBackground(OVERVIEW_DEFAULT_LEGACY_GAP);
+ }
+ else
+ {
+ gapColour.setBackground(OVERVIEW_DEFAULT_GAP);
+ }
+ gapColour.setEnabled(!enabled);
+ gapLabel.setEnabled(!enabled);
+ }
+
+ @Override
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ useLegacyGap.setSelected(false);
+ useLegacyGaps_actionPerformed(null);
+ showHiddenAtStart.setSelected(true);
+ hiddenColour.setBackground(OVERVIEW_DEFAULT_HIDDEN);
+ }
+
+ @Override
protected void userIdWidth_actionPerformed()
{
try
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
+import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
{
final FeatureRenderer fr;
- final SequenceRenderer sr;
+ final SequenceRenderer seqRdr;
BufferedImage img;
Graphics2D gg;
- int imgWidth;
-
- int imgHeight;
-
AlignViewport av;
boolean fastPaint = false;
int cursorY = 0;
+ int charHeight = 0;
+
+ int charWidth = 0;
+
+ boolean fastpainting = false;
+
+ AnnotationPanel annotations;
+
/**
* Creates a new SeqCanvas object.
*
this.av = ap.av;
updateViewport();
fr = new FeatureRenderer(ap);
- sr = new SequenceRenderer(av);
+ seqRdr = new SequenceRenderer(av);
setLayout(new BorderLayout());
PaintRefresher.Register(this, av.getSequenceSetId());
setBackground(Color.white);
public SequenceRenderer getSequenceRenderer()
{
- return sr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
return fr;
}
- int charHeight = 0, charWidth = 0;
-
private void updateViewport()
{
charHeight = av.getCharHeight();
}
}
- boolean fastpainting = false;
/**
* need to make this thread safe move alignment rendering in response to
int transX = 0;
int transY = 0;
- gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
- imgHeight, -horizontal * charWidth, -vertical * charHeight);
+ gg.copyArea(horizontal * charWidth, vertical * charHeight,
+ img.getWidth(), img.getHeight(), -horizontal * charWidth,
+ -vertical * charHeight);
if (horizontal > 0) // scrollbar pulled right, image to the left
{
}
else
{
- transY = imgHeight - ((vertical + 1) * charHeight);
+ transY = img.getHeight() - ((vertical + 1) * charHeight);
}
}
else if (vertical < 0)
@Override
public void paintComponent(Graphics g)
{
- updateViewport();
- BufferedImage lcimg = img; // take reference since other threads may null
- // img and call later.
super.paintComponent(g);
- if (lcimg != null && (fastPaint
+ updateViewport();
+
+ ViewportRanges ranges = av.getRanges();
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ // selectImage is the selection group outline image
+ BufferedImage selectImage = drawSelectionGroup(
+ ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq());
+
+ if ((img != null) && (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height)))
{
+ BufferedImage lcimg = buildLocalImage(selectImage);
g.drawImage(lcimg, 0, 0, this);
fastPaint = false;
- return;
}
+ else if ((width > 0) && (height > 0))
+ {
+ // img is a cached version of the last view we drew, if any
+ // if we have no img or the size has changed, make a new one
+ if (img == null || width != img.getWidth()
+ || height != img.getHeight())
+ {
+ img = setupImage();
+ if (img == null)
+ {
+ return;
+ }
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ }
- // this draws the whole of the alignment
- imgWidth = getWidth();
- imgHeight = getHeight();
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
- imgWidth -= (imgWidth % charWidth);
- imgHeight -= (imgHeight % charHeight);
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, img.getWidth(), img.getHeight());
- if ((imgWidth < 1) || (imgHeight < 1))
- {
- return;
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ }
+ else
+ {
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ }
+
+ // lcimg is a local *copy* of img which we'll draw selectImage on top of
+ BufferedImage lcimg = buildLocalImage(selectImage);
+ g.drawImage(lcimg, 0, 0, this);
}
+ }
+
+ /**
+ * Draw an alignment panel for printing
+ *
+ * @param g1
+ * Graphics object to draw with
+ * @param startRes
+ * start residue of print area
+ * @param endRes
+ * end residue of print area
+ * @param startSeq
+ * start sequence of print area
+ * @param endSeq
+ * end sequence of print area
+ */
+ public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+ startSeq, endSeq);
+ drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+ ((Graphics2D) g1).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g1.drawImage(selectImage, 0, 0, this);
+ }
- if (lcimg == null || imgWidth != lcimg.getWidth()
- || imgHeight != lcimg.getHeight())
+ /**
+ * Draw a wrapped alignment panel for printing
+ *
+ * @param g
+ * Graphics object to draw with
+ * @param canvasWidth
+ * width of drawing area
+ * @param canvasHeight
+ * height of drawing area
+ * @param startRes
+ * start residue of print area
+ */
+ public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ SequenceGroup group = av.getSelectionGroup();
+
+ drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+
+ if (group != null)
{
+ BufferedImage selectImage = null;
try
{
- lcimg = img = new BufferedImage(imgWidth, imgHeight,
- BufferedImage.TYPE_INT_RGB);
- gg = (Graphics2D) img.getGraphics();
- gg.setFont(av.getFont());
+ selectImage = new BufferedImage(canvasWidth, canvasHeight,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
} catch (OutOfMemoryError er)
{
System.gc();
- System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
- new OOMWarning("Creating alignment image for display", er);
-
- return;
+ System.err.println("Print image OutOfMemory Error.\n" + er);
+ new OOMWarning("Creating wrapped alignment image for printing", er);
+ }
+ if (selectImage != null)
+ {
+ Graphics2D g2 = selectImage.createGraphics();
+ setupSelectionGroup(g2, selectImage);
+ drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
+ startRes);
+
+ g2.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g.drawImage(selectImage, 0, 0, this);
+ g2.dispose();
}
}
+ }
- if (av.antiAlias)
+ /*
+ * Make a local image by combining the cached image img
+ * with any selection
+ */
+ private BufferedImage buildLocalImage(BufferedImage selectImage)
+ {
+ // clone the cached image
+ BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+ img.getType());
+ Graphics2D g2d = lcimg.createGraphics();
+ g2d.drawImage(img, 0, 0, null);
+
+ // overlay selection group on lcimg
+ if (selectImage != null)
{
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ g2d.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+ g2d.drawImage(selectImage, 0, 0, this);
}
+ g2d.dispose();
- gg.setColor(Color.white);
- gg.fillRect(0, 0, imgWidth, imgHeight);
+ return lcimg;
+ }
- ViewportRanges ranges = av.getRanges();
- if (av.getWrapAlignment())
+ /*
+ * Set up a buffered image of the correct height and size for the sequence canvas
+ */
+ private BufferedImage setupImage()
+ {
+ BufferedImage lcimg = null;
+
+ int width = getWidth();
+ int height = getHeight();
+
+ width -= (width % charWidth);
+ height -= (height % charHeight);
+
+ if ((width < 1) || (height < 1))
{
- drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ return null;
}
- else
+
+ try
{
- drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
- ranges.getStartSeq(), ranges.getEndSeq(), 0);
- }
+ lcimg = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println(
+ "Group image OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
- g.drawImage(lcimg, 0, 0, this);
+ return null;
+ }
+ return lcimg;
}
/**
* @param startRes
* DOCUMENT ME!
*/
- public void drawWrappedPanel(Graphics g, int canvasWidth,
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
updateViewport();
}
}
- AnnotationPanel annotations;
+ /*
+ * Draw a selection group over a wrapped alignment
+ */
+ private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
+ int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ // height gap above each panel
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ int startx = startRes;
+ int endx;
+ int ypos = hgap; // vertical offset
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ // chop the wrapped alignment extent up into panel-sized blocks and treat
+ // each block as if it were a block from an unwrapped alignment
+ while ((ypos <= canvasHeight) && (startx < maxwidth))
+ {
+ // set end value to be start + width, or maxwidth, whichever is smaller
+ endx = startx + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ drawUnwrappedSelection(g, group, startx, endx, 0,
+ av.getAlignment().getHeight() - 1,
+ ypos);
+
+ g.translate(-LABEL_WEST, 0);
+
+ // update vertical offset
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ // update horizontal offset
+ startx += cWidth;
+ }
+ }
int getAnnotationHeight()
{
return annotations.adjustPanelHeight();
}
- /**
- * DOCUMENT ME!
+ /*
+ * Draw an alignment panel for printing
*
* @param g1
- * DOCUMENT ME!
+ * Graphics object to draw with
* @param startRes
- * DOCUMENT ME!
+ * start residue of print area
* @param endRes
- * DOCUMENT ME!
+ * end residue of print area
* @param startSeq
- * DOCUMENT ME!
+ * start sequence of print area
* @param endSeq
- * DOCUMENT ME!
+ * end sequence of print area
* @param offset
- * DOCUMENT ME!
+ * vertical offset
*/
- public void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ private void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
updateViewport();
if (!av.hasHiddenColumns())
}
- // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
- // int x1, int x2, int y1, int y2, int startx, int starty,
private void draw(Graphics g, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.isRenderGaps());
+ seqRdr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
// empty
continue;
}
- sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * charHeight));
if (av.isShowSequenceFeatures())
{
for (int r = 0; r < visibleResults.length; r += 2)
{
- sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1],
- (visibleResults[r] - startRes) * charWidth,
- offset + ((i - startSeq) * charHeight));
+ seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
offset + ((i - startSeq) * charHeight));
}
}
// ///////////////////////////////////
// Now outline any areas if necessary
// ///////////////////////////////////
- SequenceGroup group = av.getSelectionGroup();
- int sx = -1;
- int sy = -1;
- int ex = -1;
+ SequenceGroup group = null;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * charWidth;
- if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ if (av.getAlignment().getGroups().size() > 0)
{
group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
if (group != null)
{
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+
do
{
- int oldY = -1;
- int i = 0;
- boolean inGroup = false;
- int top = -1;
- int bottom = -1;
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+ endSeq, offset);
+
+ groupIndex++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private BufferedImage drawSelectionGroup(int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+ // get a new image of the correct size
+ BufferedImage selectionImage = setupImage();
+
+ if (selectionImage == null)
+ {
+ return null;
+ }
+
+ SequenceGroup group = av.getSelectionGroup();
+ if (group == null)
+ {
+ // nothing to draw
+ return null;
+ }
+
+ // set up drawing colour
+ Graphics2D g = (Graphics2D) selectionImage.getGraphics();
+
+ setupSelectionGroup(g, selectionImage);
+
+ if (!av.getWrapAlignment())
+ {
+ drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq,
+ 0);
+ }
+ else
+ {
+ drawWrappedSelection(g, group, getWidth(), getHeight(),
+ av.getRanges().getStartRes());
+ }
+
+ g.dispose();
+ return selectionImage;
+ }
+
+ /*
+ * Set up graphics for selection group
+ */
+ private void setupSelectionGroup(Graphics2D g,
+ BufferedImage selectionImage)
+ {
+ // set background to transparent
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
+ g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
+
+ // set up foreground to draw red dashed line
+ g.setComposite(AlphaComposite.Src);
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[]
+ { 5f, 3f }, 0f));
+ g.setColor(Color.RED);
+ }
+
+ /*
+ * Draw a selection group over an unwrapped alignment
+ * @param g graphics object to draw with
+ * @param group selection group
+ * @param startRes start residue of area to draw
+ * @param endRes end residue of area to draw
+ * @param startSeq start sequence of area to draw
+ * @param endSeq end sequence of area to draw
+ * @param offset vertical offset (used when called from wrapped alignment code)
+ */
+ private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq, int offset)
+ {
+ if (!av.hasHiddenColumns())
+ {
+ drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
+ offset);
+ }
+ else
+ {
+ // package into blocks of visible columns
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
- for (i = startSeq; i <= endSeq; i++)
+ if (hideStart <= blockStart)
{
- sx = (group.getStartRes() - startRes) * charWidth;
- sy = offset + ((i - startSeq) * charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
- - 1;
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
- if (sx + ex < 0 || sx > visWidth)
- {
- continue;
- }
+ blockEnd = hideStart - 1;
- if ((sx <= (endRes - startRes) * charWidth)
- && group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i)))
- {
- if ((bottom == -1) && !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i + 1)))
- {
- bottom = sy + 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.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
- g.setColor(Color.RED);
- }
- else
- {
- g.setStroke(new BasicStroke());
- g.setColor(group.getOutlineColour());
- }
- }
- }
- else
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > (endRes - startRes))
+ {
+ // already rendered last block
+ break;
+ }
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g.translate(screenY * charWidth, 0);
+ drawPartialGroupOutline(g, group,
+ blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g.translate(-screenY * charWidth, 0);
+ }
+ }
+ }
+
+ /*
+ * Draw the selection group as a separate image and overlay
+ */
+ private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
+ int startRes, int endRes, int startSeq, int endSeq,
+ int verticalOffset)
+ {
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+
+ int sx = -1;
+ int sy = -1;
+ int xwidth = -1;
+
+ for (i = startSeq; i <= endSeq; i++)
+ {
+ // position of start residue of group relative to startRes, in pixels
+ sx = (group.getStartRes() - startRes) * charWidth;
+
+ // width of group in pixels
+ xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
+ - 1;
+
+ sy = verticalOffset + (i - startSeq) * charHeight;
+
+ if (sx + xwidth < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1) && !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
- if (inGroup)
- {
- if (sx >= 0 && sx < visWidth)
- {
- g.drawLine(sx, oldY, sx, sy);
- }
-
- if (sx + ex < visWidth)
- {
- g.drawLine(sx + ex, oldY, sx + ex, sy);
- }
-
- if (sx < 0)
- {
- ex += sx;
- sx = 0;
- }
-
- if (sx + ex > visWidth)
- {
- ex = visWidth;
- }
-
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * 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;
- }
+ top = sy;
}
- }
+ oldY = sy;
+ inGroup = true;
+ }
+ }
+ else
+ {
if (inGroup)
{
- sy = offset + ((i - startSeq) * charHeight);
+ // if start position is visible, draw vertical line to left of
+ // group
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
}
- if (sx + ex < visWidth)
+ // if end position is visible, draw vertical line to right of
+ // group
+ if (sx + xwidth < visWidth)
{
- g.drawLine(sx + ex, oldY, sx + ex, sy);
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
if (sx < 0)
{
- ex += sx;
+ xwidth += sx;
sx = 0;
}
- if (sx + ex > visWidth)
+ // don't let width extend beyond current block, or group extent
+ // fixes JAL-2672
+ if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
{
- ex = visWidth;
+ xwidth = (endRes - startRes + 1) * charWidth - sx;
}
- else if (sx + ex >= (endRes - startRes + 1) * charWidth)
- {
- ex = (endRes - startRes + 1) * charWidth;
- }
-
+
+ // draw horizontal line at top of group
if (top != -1)
{
- g.drawLine(sx, top, sx + ex, top);
+ g.drawLine(sx, top, sx + xwidth, top);
top = -1;
}
+ // draw horizontal line at bottom of group
if (bottom != -1)
{
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+ g.drawLine(sx, bottom, sx + xwidth, bottom);
bottom = -1;
}
inGroup = false;
}
+ }
+ }
- groupIndex++;
+ if (inGroup)
+ {
+ sy = verticalOffset + ((i - startSeq) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
- g.setStroke(new BasicStroke());
+ if (sx + xwidth < visWidth)
+ {
+ g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+ }
- if (groupIndex >= av.getAlignment().getGroups().size())
- {
- break;
- }
+ if (sx < 0)
+ {
+ xwidth += sx;
+ sx = 0;
+ }
- group = av.getAlignment().getGroups().get(groupIndex);
+ if (sx + xwidth > visWidth)
+ {
+ xwidth = visWidth;
+ }
+ else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
+ {
+ xwidth = (endRes - startRes + 1) * charWidth;
+ }
- } while (groupIndex < av.getAlignment().getGroups().size());
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + xwidth, top);
+ top = -1;
+ }
- }
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
+ bottom = -1;
+ }
+ inGroup = false;
+ }
}
-
+
/**
* DOCUMENT ME!
*
{
String eventName = evt.getPropertyName();
- if (av.getWrapAlignment())
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ }
+ else if (av.getWrapAlignment())
{
if (eventName.equals(ViewportRanges.STARTRES))
{
if (stretchGroup == null)
{
- // Only if left mouse button do we want to change group sizes
+ createStretchGroup(res, sequence);
+ }
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- stretchGroup = sg;
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
- if (av.getConservationSelected())
- {
- SliderPanel.setConservationSlider(ap, av.getResidueShading(),
- ap.getViewName());
- }
+ seqCanvas.repaint();
+ }
- if (av.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
- ap.getViewName());
- }
- // TODO: stretchGroup will always be not null. Is this a merge error ?
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ((stretchGroup != null)
- && (stretchGroup.getStartRes() == res))
- {
- // Edit end res position of selected group
- changeStartRes = true;
- }
- stretchGroup.getWidth();
+ private void createStretchGroup(int res, SequenceI sequence)
+ {
+ // Only if left mouse button do we want to change group sizes
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
}
- seqCanvas.repaint();
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
+ // or is there a threading issue here?
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+
}
/**
{
return;
}
+
+ stretchGroup.removePropertyChangeListener(seqCanvas);
+
// always do this - annotation has own state
// but defer colourscheme update until hidden sequences are passed in
boolean vischange = stretchGroup.recalcConservation(true);
{
scrollThread.setEvent(evt);
}
-
- seqCanvas.repaint();
}
void scrollCanvas(MouseEvent evt)
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
+import jalview.renderer.ResidueColourFinder;
import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.util.Comparison;
import java.awt.Color;
import java.awt.FontMetrics;
boolean renderGaps = true;
- SequenceGroup currentSequenceGroup = null;
-
SequenceGroup[] allGroups = null;
- Color resBoxColour;
+ // Color resBoxColour;
Graphics graphics;
boolean monospacedFont;
- boolean forOverview = false;
+ ResidueColourFinder resColourFinder;
/**
* Creates a new SequenceRenderer object
public SequenceRenderer(AlignViewportI viewport)
{
this.av = viewport;
+ resColourFinder = new ResidueColourFinder();
}
/**
this.renderGaps = renderGaps;
}
- protected Color getResidueBoxColour(SequenceI seq, int i)
- {
- // rate limiting step when rendering overview for lots of groups
- allGroups = av.getAlignment().findAllGroups(seq);
-
- if (inCurrentSequenceGroup(i))
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.getResidueShading(), seq, i);
- }
-
- return resBoxColour;
- }
-
/**
* Get the residue colour at the given sequence position - as determined by
* the sequence group colour (if any), else the colour scheme, possibly
public Color getResidueColour(final SequenceI seq, int position,
FeatureColourFinder finder)
{
- Color col = getResidueBoxColour(seq, position);
-
- if (finder != null)
- {
- col = finder.findFeatureColour(col, seq, position);
- }
- return col;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param shader
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param i
- * DOCUMENT ME!
- */
- void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
- {
- if (shader.getColourScheme() != null)
- {
- resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
- }
- else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
- {
- resBoxColour = Color.lightGray;
- }
- else
- {
- resBoxColour = Color.white;
- }
+ return resColourFinder.getResidueColour(av.getShowBoxes(),
+ av.getResidueShading(),
+ allGroups, seq, position,
+ finder);
}
/**
public synchronized void drawBoxes(SequenceI seq, int start, int end,
int y1)
{
+ Color resBoxColour = Color.white;
+
if (seq == null)
{
return; // fix for racecondition
if (i < length)
{
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
+ if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
}
boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
boolean isarep = av.getAlignment().getSeqrep() == seq;
- boolean isgrep = currentSequenceGroup != null
- ? currentSequenceGroup.getSeqrep() == seq
- : false;
- char sr_c;
+ Color resBoxColour = Color.white;
+
for (int i = start; i <= end; i++)
{
continue;
}
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
+ if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
if (currentSequenceGroup.getColourText())
{
graphics.setColor(currentSequenceGroup.textColour);
}
+ boolean isgrep = currentSequenceGroup != null
+ ? currentSequenceGroup.getSeqrep() == seq : false;
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
{
if (!getboxColour)
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
/**
* DOCUMENT ME!
*
- * @param res
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- boolean inCurrentSequenceGroup(int res)
- {
- if (allGroups == null)
- {
- return false;
- }
-
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- currentSequenceGroup = allGroups[i];
-
- return true;
- }
- }
-
- return false;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param seq
* DOCUMENT ME!
* @param start
protected JCheckBox rightAlign = new JCheckBox();
- protected JComboBox<String> fontSizeCB = new JComboBox<String>();
+ protected JComboBox<String> fontSizeCB = new JComboBox<>();
- protected JComboBox<String> fontStyleCB = new JComboBox<String>();
+ protected JComboBox<String> fontStyleCB = new JComboBox<>();
- protected JComboBox<String> fontNameCB = new JComboBox<String>();
+ protected JComboBox<String> fontNameCB = new JComboBox<>();
protected JCheckBox showOccupancy = new JCheckBox();
protected JCheckBox scaleProteinToCdna = new JCheckBox();
- protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
+ protected JComboBox<String> gapSymbolCB = new JComboBox<>();
protected JCheckBox wrap = new JCheckBox();
- protected JComboBox<String> sortby = new JComboBox<String>();
+ protected JComboBox<String> sortby = new JComboBox<>();
- protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+ protected JComboBox<String> sortAnnBy = new JComboBox<>();
- protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+ protected JComboBox<String> sortAutocalc = new JComboBox<>();
protected JCheckBox startupCheckbox = new JCheckBox();
protected JCheckBox addTempFactor = new JCheckBox();
- protected JComboBox<String> structViewer = new JComboBox<String>();
+ protected JComboBox<String> structViewer = new JComboBox<>();
protected JTextField chimeraPath = new JTextField();
protected JPanel maxColour = new JPanel();
- protected JComboBox<String> protColour = new JComboBox<String>();
+ protected JComboBox<String> protColour = new JComboBox<>();
- protected JComboBox<String> nucColour = new JComboBox<String>();
+ protected JComboBox<String> nucColour = new JComboBox<>();
+
+ /*
+ * Overview tab components
+ */
+ protected JPanel gapColour = new JPanel();
+
+ protected JPanel hiddenColour = new JPanel();
+
+ protected JCheckBox useLegacyGap;
+
+ protected JCheckBox showHiddenAtStart;
+
+ protected JLabel gapLabel;
/*
* Connections tab components
/*
* Output tab components
*/
- protected JComboBox<Object> epsRendering = new JComboBox<Object>();
+ protected JComboBox<Object> epsRendering = new JComboBox<>();
protected JLabel userIdWidthlabel = new JLabel();
tabbedPane.add(initColoursTab(),
MessageManager.getString("label.colours"));
+ tabbedPane.add(initOverviewTab(),
+ MessageManager.getString("label.overview"));
+
tabbedPane.add(initStructureTab(),
MessageManager.getString("label.structure"));
}
/**
+ * Initialises the Overview tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initOverviewTab()
+ {
+ JPanel overviewPanel = new JPanel();
+ overviewPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.overview_settings")));
+
+ gapColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ gapColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ gapColour.setPreferredSize(new Dimension(40, 20));
+ gapColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ gapColour_actionPerformed(gapColour);
+ }
+ });
+
+ hiddenColour.setFont(LABEL_FONT);
+ // fixing the border colours stops apparent colour bleed from the panel
+ hiddenColour.setBorder(
+ BorderFactory.createEtchedBorder(Color.white, Color.lightGray));
+ hiddenColour.setPreferredSize(new Dimension(40, 20));
+ hiddenColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ hiddenColour_actionPerformed(hiddenColour);
+ }
+ });
+
+ useLegacyGap = new JCheckBox(
+ MessageManager.getString("label.ov_legacy_gap"));
+ useLegacyGap.setFont(LABEL_FONT);
+ useLegacyGap.setHorizontalAlignment(SwingConstants.LEFT);
+ useLegacyGap.setVerticalTextPosition(SwingConstants.TOP);
+ gapLabel = new JLabel(
+ MessageManager.getString("label.gap_colour"));
+ gapLabel.setFont(LABEL_FONT);
+ gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ gapLabel.setVerticalTextPosition(SwingConstants.TOP);
+ showHiddenAtStart = new JCheckBox(
+ MessageManager.getString("label.ov_show_hide_default"));
+ showHiddenAtStart.setFont(LABEL_FONT);
+ showHiddenAtStart.setHorizontalAlignment(SwingConstants.LEFT);
+ showHiddenAtStart.setVerticalTextPosition(SwingConstants.TOP);
+ JLabel hiddenLabel = new JLabel(
+ MessageManager.getString("label.hidden_colour"));
+ hiddenLabel.setFont(LABEL_FONT);
+ hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ hiddenLabel.setVerticalTextPosition(SwingConstants.TOP);
+
+ useLegacyGap.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ useLegacyGaps_actionPerformed(e);
+ }
+ });
+
+ overviewPanel.setLayout(new GridBagLayout());
+ GridBagConstraints c1 = new GridBagConstraints();
+
+ c1.fill = GridBagConstraints.HORIZONTAL;
+ c1.gridx = 0;
+ c1.gridy = 0;
+ c1.weightx = 1;
+ c1.ipady = 20;
+ c1.anchor = GridBagConstraints.FIRST_LINE_START;
+ overviewPanel.add(useLegacyGap, c1);
+
+ GridBagConstraints c2 = new GridBagConstraints();
+ c2.fill = GridBagConstraints.HORIZONTAL;
+ c2.gridx = 1;
+ c2.gridy = 0;
+ c2.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(gapLabel, c2);
+
+ GridBagConstraints c3 = new GridBagConstraints();
+ c3.fill = GridBagConstraints.HORIZONTAL;
+ c3.gridx = 2;
+ c3.gridy = 0;
+ c3.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(gapColour, c3);
+
+ GridBagConstraints c4 = new GridBagConstraints();
+ c4.fill = GridBagConstraints.HORIZONTAL;
+ c4.gridx = 0;
+ c4.gridy = 1;
+ c4.weightx = 1;
+ overviewPanel.add(showHiddenAtStart, c4);
+
+ GridBagConstraints c5 = new GridBagConstraints();
+ c5.fill = GridBagConstraints.HORIZONTAL;
+ c5.gridx = 1;
+ c5.gridy = 1;
+ c5.insets = new Insets(0, 15, 0, 10);
+ overviewPanel.add(hiddenLabel, c5);
+
+ GridBagConstraints c6 = new GridBagConstraints();
+ c6.fill = GridBagConstraints.HORIZONTAL;
+ c6.gridx = 2;
+ c6.gridy = 1;
+ c6.insets = new Insets(0, 0, 0, 15);
+ overviewPanel.add(hiddenColour, c6);
+
+ JButton resetButton = new JButton(
+ MessageManager.getString("label.reset_to_defaults"));
+
+ resetButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ resetOvDefaults_actionPerformed(e);
+ }
+ });
+
+ GridBagConstraints c7 = new GridBagConstraints();
+ c7.fill = GridBagConstraints.NONE;
+ c7.gridx = 0;
+ c7.gridy = 2;
+ c7.insets = new Insets(10, 0, 0, 0);
+ c7.anchor = GridBagConstraints.WEST;
+ overviewPanel.add(resetButton, c7);
+
+ // Add padding so the panel doesn't look ridiculous
+ JPanel spacePanel = new JPanel();
+ overviewPanel.add(spacePanel,
+ new GridBagConstraints(0, 3, 1, 1, 1.0, 1.0,
+ GridBagConstraints.WEST, GridBagConstraints.BOTH,
+ new Insets(0, 0, 0, 5), 0, 0));
+
+ return overviewPanel;
+ }
+
+ /**
* Initialises the Structure tabbed panel.
*
* @return
{
}
+ protected void gapColour_actionPerformed(JPanel panel)
+ {
+ }
+
+ protected void hiddenColour_actionPerformed(JPanel panel)
+ {
+ }
+
protected void showunconserved_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
}
+ protected void useLegacyGaps_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void resetOvDefaults_actionPerformed(ActionEvent e)
+ {
+ }
+
/**
* DOCUMENT ME!
*
import jalview.api.AlignmentColsCollectionI;
import jalview.api.AlignmentRowsCollectionI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.viewmodel.OverviewDimensions;
+import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.Graphics;
+import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
public class OverviewRenderer
{
- private FeatureColourFinder finder;
+ // transparency of hidden cols/seqs overlay
+ private final float TRANSPARENCY = 0.5f;
+
+ private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
- private jalview.api.SequenceRenderer sr;
+ private FeatureColourFinder finder;
// image to render on
private BufferedImage miniMe;
// flag to indicate whether to halt drawing
private volatile boolean redraw = false;
- public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
- FeatureRenderer fr, OverviewDimensions od)
+ // reference to alignment, needed to get sequence groups
+ private AlignmentI al;
+
+ private ResidueShaderI shader;
+
+ private OverviewResColourFinder resColFinder;
+
+ public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
+ AlignmentI alignment,
+ ResidueShaderI resshader, OverviewResColourFinder colFinder)
{
- sr = seqRenderer;
finder = new FeatureColourFinder(fr);
+ resColFinder = colFinder;
+
+ al = alignment;
+ shader = resshader;
pixelsPerCol = od.getPixelsPerCol();
pixelsPerSeq = od.getPixelsPerSeq();
{
break;
}
-
+
// get details of this alignment row
- boolean hidden = rows.isHidden(alignmentRow);
SequenceI seq = rows.getSequence(alignmentRow);
+ // rate limiting step when rendering overview for lots of groups
+ SequenceGroup[] allGroups = al.findAllGroups(seq);
+
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
miniMe.getHeight() - 1);
-
+
int colIndex = 0;
int pixelCol = 0;
for (int alignmentCol : cols)
{
break;
}
-
+
// calculate where this column extends to in pixels
int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
-
+
// don't do expensive colour determination if we're not going to use it
// NB this is important to avoid performance issues in the overview
// panel
if (pixelCol <= endCol)
{
- // determine the colour based on the sequence and column position
- rgbcolor = getColumnColourFromSequence(seq,
- hidden || cols.isHidden(alignmentCol), alignmentCol,
- finder);
-
+ rgbcolor = getColumnColourFromSequence(allGroups, seq,
+ alignmentCol, finder);
+
// fill in the appropriate number of pixels
for (int row = pixelRow; row <= endRow; ++row)
{
miniMe.setRGB(col, row, rgbcolor);
}
}
-
+
pixelCol = endCol + 1;
}
colIndex++;
pixelRow = endRow + 1;
seqIndex++;
}
+
+ overlayHiddenRegions(rows, cols);
return miniMe;
}
- /*
+ /**
* Find the colour of a sequence at a specified column position
+ *
+ * @param seq
+ * sequence to get colour for
+ * @param lastcol
+ * column position to get colour for
+ * @param fcfinder
+ * FeatureColourFinder to use
+ * @return colour of sequence at this position, as RGB
*/
- private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
+ private int getColumnColourFromSequence(SequenceGroup[] allGroups,
+ jalview.datamodel.SequenceI seq,
+ int lastcol, FeatureColourFinder fcfinder)
{
Color color = Color.white;
if ((seq != null) && (seq.getLength() > lastcol))
{
- color = sr.getResidueColour(seq, lastcol, fcfinder);
+ color = resColFinder.getResidueColour(true, shader, allGroups, seq,
+ lastcol,
+ fcfinder);
}
- if (isHidden)
+ return color.getRGB();
+ }
+
+ /**
+ * Overlay the hidden regions on the overview image
+ *
+ * @param rows
+ * collection of rows the overview is built over
+ * @param cols
+ * collection of columns the overview is built over
+ */
+ private void overlayHiddenRegions(AlignmentRowsCollectionI rows,
+ AlignmentColsCollectionI cols)
+ {
+ if (cols.hasHidden() || rows.hasHidden())
{
- color = color.darker().darker();
+ BufferedImage mask = buildHiddenImage(rows, cols, miniMe.getWidth(),
+ miniMe.getHeight());
+
+ Graphics2D g = (Graphics2D) miniMe.getGraphics();
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ TRANSPARENCY));
+ g.drawImage(mask, 0, 0, miniMe.getWidth(), miniMe.getHeight(), null);
}
+ }
- return color.getRGB();
+ /**
+ * Build a masking image of hidden columns and rows to be applied on top of
+ * the main overview image.
+ *
+ * @param rows
+ * collection of rows the overview is built over
+ * @param cols
+ * collection of columns the overview is built over
+ * @param width
+ * width of overview in pixels
+ * @param height
+ * height of overview in pixels
+ * @return BufferedImage containing mask of hidden regions
+ */
+ private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows,
+ AlignmentColsCollectionI cols, int width, int height)
+ {
+ // new masking image
+ BufferedImage hiddenImage = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_ARGB);
+
+ int colIndex = 0;
+ int pixelCol = 0;
+
+ Color hidden = resColFinder.getHiddenColour();
+
+ Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
+
+ // set background to transparent
+ g2d.setComposite(AlphaComposite.Clear);
+ g2d.fillRect(0, 0, width, height);
+
+ // set next colour to opaque
+ g2d.setComposite(AlphaComposite.Src);
+
+ for (int alignmentCol : cols)
+ {
+ if (redraw)
+ {
+ break;
+ }
+
+ // calculate where this column extends to in pixels
+ int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ hiddenImage.getWidth() - 1);
+
+ if (pixelCol <= endCol)
+ {
+ // determine the colour based on the sequence and column position
+ if (cols.isHidden(alignmentCol))
+ {
+ g2d.setColor(hidden);
+ g2d.fillRect(pixelCol, 0, endCol - pixelCol + 1, height);
+ }
+
+ pixelCol = endCol + 1;
+ }
+ colIndex++;
+
+ }
+
+ int seqIndex = 0;
+ int pixelRow = 0;
+ for (int alignmentRow : rows)
+ {
+ if (redraw)
+ {
+ break;
+ }
+
+ // calculate where this row extends to in pixels
+ int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
+ miniMe.getHeight() - 1);
+
+ // get details of this alignment row
+ if (rows.isHidden(alignmentRow))
+ {
+ g2d.setColor(hidden);
+ g2d.fillRect(0, pixelRow, width, endRow - pixelRow + 1);
+ }
+ pixelRow = endRow + 1;
+ seqIndex++;
+ }
+
+ return hiddenImage;
}
/**
}
}
+ /**
+ * Allows redraw flag to be set
+ *
+ * @param b
+ * value to set redraw to: true = redraw is occurring, false = no
+ * redraw
+ */
public void setRedraw(boolean b)
{
synchronized (this)
--- /dev/null
+/*
+ * 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.renderer;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+
+public class OverviewResColourFinder extends ResidueColourFinder
+{
+ final Color GAP_COLOUR; // default colour to use at gaps
+
+ final Color RESIDUE_COLOUR; // default colour to use at residues
+
+ final Color HIDDEN_COLOUR; // colour for hidden regions
+
+ boolean useLegacy = false;
+
+ /**
+ * Constructor without colour settings (used by applet)
+ */
+ public OverviewResColourFinder()
+ {
+ this(false, Preferences.OVERVIEW_DEFAULT_GAP,
+ Preferences.OVERVIEW_DEFAULT_HIDDEN);
+ }
+
+ /**
+ * Constructor with colour settings
+ *
+ * @param useLegacyColouring
+ * whether to use legacy gap colouring (white gaps, grey residues)
+ * @param gapCol
+ * gap colour if not legacy
+ * @param hiddenCol
+ * hidden region colour (transparency applied by rendering code)
+ */
+ public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
+ Color hiddenCol)
+ {
+ if (useLegacyColouring)
+ {
+ GAP_COLOUR = Color.white;
+ RESIDUE_COLOUR = Color.lightGray;
+ HIDDEN_COLOUR = hiddenCol;
+ }
+ else
+ {
+ GAP_COLOUR = gapCol;
+ RESIDUE_COLOUR = Color.white;
+ HIDDEN_COLOUR = hiddenCol;
+ }
+ }
+
+ @Override
+ public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+ {
+ Color resBoxColour = RESIDUE_COLOUR;
+ char currentChar = seq.getCharAt(i);
+
+ // In the overview window, gaps are coloured grey, unless the colour scheme
+ // specifies a gap colour, in which case gaps honour the colour scheme
+ // settings
+ if (shader.getColourScheme() != null)
+ {
+ if (Comparison.isGap(currentChar)
+ && (!shader.getColourScheme().hasGapColour()))
+ {
+ resBoxColour = GAP_COLOUR;
+ }
+ else
+ {
+ resBoxColour = shader.findColour(currentChar, i, seq);
+ }
+ }
+ else if (Comparison.isGap(currentChar))
+ {
+ resBoxColour = GAP_COLOUR;
+ }
+
+ return resBoxColour;
+ }
+
+ /**
+ * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
+ * overview displays the colours regardless.
+ */
+ @Override
+ protected Color getResidueBoxColour(boolean showBoxes,
+ ResidueShaderI shader,
+ SequenceGroup[] allGroups, SequenceI seq, int i)
+ {
+ ResidueShaderI currentShader;
+ SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+ i);
+ if (currentSequenceGroup != null)
+ {
+ currentShader = currentSequenceGroup.getGroupColourScheme();
+ }
+ else
+ {
+ currentShader = shader;
+ }
+
+ return getBoxColour(currentShader, seq, i);
+ }
+
+ /**
+ * Supply hidden colour
+ *
+ * @return colour of hidden regions
+ */
+ protected Color getHiddenColour()
+ {
+ return HIDDEN_COLOUR;
+ }
+}
--- /dev/null
+/*
+ * 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.renderer;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+
+import java.awt.Color;
+
+public class ResidueColourFinder
+{
+ public ResidueColourFinder()
+ {
+ }
+
+ /**
+ * Get the colour of a residue in a sequence
+ *
+ * @param showBoxes
+ * true if the viewport's Show Boxes setting is true
+ * @param shader
+ * the viewport's colour scheme
+ * @param allGroups
+ * all the groups which seq participates in
+ * @param seq
+ * the sequence containing the residue
+ * @param position
+ * the position of the residue in the sequence
+ * @param finder
+ * FeatureColourFinder for the viewport
+ * @return colour of the residue
+ */
+ public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
+ SequenceGroup[] allGroups,
+ final SequenceI seq, int position, FeatureColourFinder finder)
+ {
+ Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq,
+ position);
+
+ // if there's a FeatureColourFinder we might override the residue colour
+ // here with feature colouring
+ if (finder != null)
+ {
+ col = finder.findFeatureColour(col, seq, position);
+ }
+ return col;
+ }
+
+ /**
+ * Get the residue colour without accounting for any features
+ *
+ * @param showBoxes
+ * true if the viewport's Show Boxes setting is true
+ * @param shader
+ * the viewport's colour scheme
+ * @param allGroups
+ * all the groups which seq participates in
+ * @param seq
+ * the sequence containing the residue
+ * @param i
+ * the position of the residue in the sequence
+ * @return
+ */
+ protected Color getResidueBoxColour(boolean showBoxes,
+ ResidueShaderI shader,
+ SequenceGroup[] allGroups,
+ SequenceI seq, int i)
+ {
+ SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+ i);
+ if (currentSequenceGroup != null)
+ {
+ if (currentSequenceGroup.getDisplayBoxes())
+ {
+ return getBoxColour(currentSequenceGroup.getGroupColourScheme(),
+ seq, i);
+ }
+ }
+ else if (showBoxes)
+ {
+ return getBoxColour(shader, seq, i);
+ }
+
+ return Color.white;
+ }
+
+ /**
+ * Search all the groups for a sequence to find the one which a given res
+ * falls into
+ *
+ * @param allGroups
+ * all the groups a sequence participates in
+ * @param res
+ * the residue to search for
+ * @return a sequence group for res, or null if no sequence group applies
+ */
+ public SequenceGroup getCurrentSequenceGroup(SequenceGroup[] allGroups,
+ int res)
+ {
+ if (allGroups == null)
+ {
+ return null;
+ }
+
+ for (int i = 0; i < allGroups.length; i++)
+ {
+ if ((allGroups[i].getStartRes() <= res)
+ && (allGroups[i].getEndRes() >= res))
+ {
+ return (allGroups[i]);
+ }
+ }
+
+ return null;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param shader
+ * the viewport's colour scheme
+ * @param seq
+ * the sequence containing the residue
+ * @param i
+ * the position of the residue in the sequence
+ */
+ public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+ {
+ Color resBoxColour = Color.white;
+ if (shader.getColourScheme() != null)
+ {
+ resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
+ }
+ return resBoxColour;
+ }
+
+}
* @return
*/
boolean isSimple();
+
+ /**
+ * Answers true if the colour scheme has a colour specified for gaps.
+ *
+ * @return
+ */
+ boolean hasGapColour();
}
{
return true;
}
+
+ /**
+ * Default method returns false. Override this to return true in colour
+ * schemes that have a colour associated with gap residues.
+ */
+ @Override
+ public boolean hasGapColour()
+ {
+ return false;
+ }
}
/*
* step 1: build a map from colours to the symbol(s) that have the colour
*/
- Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+ Map<Color, List<String>> colours = new HashMap<>();
for (char symbol = 'A'; symbol <= 'Z'; symbol++)
{
/*
* step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
*/
- List<String> residueColours = new ArrayList<String>();
+ List<String> residueColours = new ArrayList<>();
for (Entry<Color, List<String>> cols : colours.entrySet())
{
boolean first = true;
Collections.sort(residueColours);
return StringUtils.listToDelimitedString(residueColours, ";");
}
+
+ @Override
+ public boolean hasGapColour()
+ {
+ return (findColour(' ') != null);
+ }
}
File reply) throws Exception
{
EmblFile efile = null;
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
if (reply != null && reply.exists())
{
* EmbFile reads something like (e.g.) this ungrammatical phrase
* Entry: <acc> display type is either not supported or entry is not found.
*/
- List<SequenceI> peptides = new ArrayList<SequenceI>();
+ List<SequenceI> peptides = new ArrayList<>();
if (efile != null && efile.getEntries() != null)
{
for (EmblEntry entry : efile.getEntries())
*/
public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
{
- Vector<SequenceI> rseqs = new Vector<SequenceI>();
- Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
+ Vector<SequenceI> rseqs = new Vector<>();
+ Hashtable<String, List<String>> queries = new Hashtable<>();
for (DBRefEntry ref : refs)
{
- if (!queries.containsKey(ref.getSource()))
+ String canonical = DBRefUtils.getCanonicalName(ref.getSource());
+ if (!queries.containsKey(canonical))
{
- queries.put(ref.getSource(), new ArrayList<String>());
+ queries.put(canonical, new ArrayList<String>());
}
- List<String> qset = queries.get(ref.getSource());
+ List<String> qset = queries.get(canonical);
if (!qset.contains(ref.getAccessionId()))
{
qset.add(ref.getAccessionId());
continue;
}
- Stack<String> queriesLeft = new Stack<String>();
+ Stack<String> queriesLeft = new Stack<>();
queriesLeft.addAll(query);
List<DbSourceProxy> proxies = getSourceProxy(db);
for (DbSourceProxy fetcher : proxies)
{
- List<String> queriesMade = new ArrayList<String>();
- HashSet<String> queriesFound = new HashSet<String>();
+ List<String> queriesMade = new ArrayList<>();
+ HashSet<String> queriesFound = new HashSet<>();
try
{
if (fetcher.isDnaCoding() != dna)
Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
if (dblist == null)
{
- return new ArrayList<DbSourceProxy>();
+ return new ArrayList<>();
}
/*
* sort so that primary sources precede secondary
*/
- List<DbSourceProxy> dbs = new ArrayList<DbSourceProxy>(dblist.values());
+ List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
Collections.sort(dbs, proxyComparator);
return dbs;
}
{
if (fetchableDbs == null)
{
- fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
+ fetchableDbs = new Hashtable<>();
}
Map<String, DbSourceProxy> slist = fetchableDbs
.get(proxy.getDbSource());
if (slist == null)
{
fetchableDbs.put(proxy.getDbSource(),
- slist = new Hashtable<String, DbSourceProxy>());
+ slist = new Hashtable<>());
}
slist.put(proxy.getDbName(), proxy);
}
return null;
}
String[] sources = null;
- Vector<String> src = new Vector<String>();
+ Vector<String> src = new Vector<>();
Enumeration<String> dbs = fetchableDbs.keys();
while (dbs.hasMoreElements())
{
public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
{
- List<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
+ List<DbSourceProxy> prlist = new ArrayList<>();
for (String fetchable : getSupportedDb())
{
for (DbSourceProxy pr : getSourceProxy(fetchable))
+++ /dev/null
-/*
- * 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.gui;
-
-import static org.testng.AssertJUnit.assertEquals;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ZappoColourScheme;
-
-import java.awt.Color;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class SequenceRendererTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testGetResidueBoxColour_zappo()
- {
- SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
- AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
- SequenceRenderer sr = new SequenceRenderer(av);
- av.setGlobalColourScheme(new ZappoColourScheme());
-
- // @see ResidueProperties.zappo
- assertEquals(Color.pink, sr.getResidueBoxColour(seq, 0)); // M
- assertEquals(Color.green, sr.getResidueBoxColour(seq, 2)); // T
- assertEquals(Color.magenta, sr.getResidueBoxColour(seq, 5)); // G
- assertEquals(Color.orange, sr.getResidueBoxColour(seq, 12)); // F
- }
-
- @Test(groups = { "Functional" })
- public void testGetResidueBoxColour_none()
- {
- SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
- AlignmentI al = new Alignment(new SequenceI[] { seq });
- final AlignViewport av = new AlignViewport(al);
- SequenceRenderer sr = new SequenceRenderer(av);
-
- assertEquals(Color.white, sr.getResidueBoxColour(seq, 0));
- assertEquals(Color.white, sr.getResidueBoxColour(seq, 2));
-
- // set for overview
- sr.forOverview = true;
- assertEquals(Color.lightGray, sr.getResidueBoxColour(seq, 0));
- assertEquals(Color.white, sr.getResidueBoxColour(seq, 2));
- }
-
- // TODO more tests for getResidueBoxColour covering groups, feature rendering,
- // gaps, overview...
-
-}
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
public void testRetrieveAndShowCrossref() throws Exception
{
- List<String> failedDBRetr = new ArrayList<String>();
- List<String> failedXrefMenuItems = new ArrayList<String>();
- List<String> failedProjectRecoveries = new ArrayList<String>();
-
+ List<String> failedDBRetr = new ArrayList<>();
+ List<String> failedXrefMenuItems = new ArrayList<>();
+ List<String> failedProjectRecoveries = new ArrayList<>();
+ // only search for ensembl or Uniprot crossrefs
+ List<String> limit=Arrays.asList(new String[] {
+ DBRefUtils.getCanonicalName("ENSEMBL"),
+ DBRefUtils.getCanonicalName("Uniprot")});
// for every set of db queries
// retrieve db query
// verify presence of expected xrefs
// . codonframes
//
//
- HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
- List<String> keyseq = new ArrayList<String>();
- HashMap<String, File> savedProjects = new HashMap<String, File>();
+ HashMap<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ HashMap<String, File> savedProjects = new HashMap<>();
- for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
- { "UNIPROT", "P01731" } })
+ for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
{
// pass counters - 0 - first pass, 1 means retrieve project rather than
// perform action
ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
seqs, dataset).findXrefSourcesForSequences(dna);
-
+ filterDbRefs(ptypes, limit);
+
// start of pass2: retrieve each cross-ref for fetched or restored
// project.
do // first cross ref and recover crossref loop
// build next key so we an retrieve all views
String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
// perform crossref action, or retrieve stored project
- List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views = new ArrayList<>();
CrossRefAction cra = null;
if (pass2 == 0)
}
}
- HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
// first save/verify views.
for (AlignmentViewPanel avp : cra_views)
{
nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
for (String xrefdb : xrptypes.get(nextxref))
{
- List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
int q = 0;
String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ q + "}";
}
}
+ private void filterDbRefs(List<String> ptypes, List<String> limit)
+ {
+ if (limit != null)
+ {
+ int p = 0;
+ while (ptypes.size() > p)
+ {
+ if (!limit.contains(ptypes.get(p)))
+ {
+ ptypes.remove(p);
+ }
+ else
+ {
+ p++;
+ }
+ }
+ }
+ }
+
/**
* wrapper to trap known defect for AH002001 testcase
*
private void assertType(boolean expectProtein,
AlignmentViewPanel alignmentViewPanel, String message)
{
- List<SequenceI> nonType = new ArrayList<SequenceI>();
+ List<SequenceI> nonType = new ArrayList<>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
.getAlignment().getSequences())
{
--- /dev/null
+/*
+ * 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.renderer;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class OverviewResColourFinderTest
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueBoxColour_none()
+ {
+ SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+
+ // gaps are grey, residues white
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(),
+ null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf
+ .getResidueColour(true, av.getResidueShading(), null, seq, 2,
+ null));
+
+ // unaffected by showBoxes setting
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueBoxColour_zappo()
+ {
+ SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
+ // gap
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+ av.setGlobalColourScheme(new ZappoColourScheme());
+
+ // @see ResidueProperties.zappo
+ assertEquals(Color.pink,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 0, null)); // M
+ assertEquals(Color.green,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 2, null)); // T
+ assertEquals(Color.magenta,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 5, null)); // G
+ assertEquals(Color.orange,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 12, null)); // F
+
+ // gap colour not specified so gaps are lightGray
+ assertEquals(Color.lightGray, rcf
+ .getResidueColour(true, av.getResidueShading(), null, seq, 3,
+ null));
+
+ // unaffected by showBoxes setting
+ assertEquals(Color.pink, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 12, null)); // F
+
+ // gap colour not specified so gaps are lightGray
+ assertEquals(Color.lightGray, rcf
+ .getResidueColour(false, av.getResidueShading(), null, seq, 3,
+ null));
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueBoxColour_userdef()
+ {
+ SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
+ // gap
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+
+ Color[] newColours = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = null;
+ }
+
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour not specified so gaps are lightGray
+ assertEquals(Color.lightGray, rcf
+ .getResidueColour(true, av.getResidueShading(), null, seq, 3,
+ null));
+
+ newColours[23] = Color.pink;
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour specified as pink
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(),
+ null, seq, 3, null));
+
+ // unaffected by showBoxes setting
+ // gap colour not specified so gaps are lightGray
+ newColours[23] = null;
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
+
+ newColours[23] = Color.pink;
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour specified as pink
+ assertEquals(Color.pink, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
+ }
+
+ @Test
+ public void testGetResidueBoxColour_group()
+ {
+ SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+
+ ColourSchemeI cs = new ZappoColourScheme();
+ ArrayList<SequenceI> seqlist = new ArrayList<>();
+ seqlist.add(seq);
+ SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
+ true, true, 5, 9);
+ al.addGroup(sg);
+ SequenceGroup[] groups = new SequenceGroup[1];
+ groups[0] = sg;
+
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use legacy colouring
+ rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured lightgray
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+
+ // use new colouring
+ rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+
+ // G in group specified as magenta in Zappo
+ assertEquals(Color.magenta, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 7, null));
+
+ // Residue outside group coloured white
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 0, null));
+
+ // Gap outside group coloured blue
+ assertEquals(Color.blue, rcf.getResidueColour(false,
+ av.getResidueShading(), groups, seq, 2, null));
+ }
+
+ @Test
+ public void testGetBoxColour()
+ {
+ SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
+ // gap
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+
+ // non-legacy colouring
+ ResidueColourFinder rcf = new OverviewResColourFinder();
+ ResidueShaderI shader = new ResidueShader();
+
+ // residues white
+ Color c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.white, c);
+
+ // gaps gap colour
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+
+ // legacy colouring set explicitly via constructor
+ rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ shader = new ResidueShader();
+
+ // residues light gray
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.lightGray, c);
+
+ // gaps white
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.white, c);
+
+ // legacy colouring off
+ rcf = new OverviewResColourFinder();
+ shader = new ResidueShader();
+
+ // residues white
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.white, c);
+
+ // gaps gap colour
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+
+ // non legacy colouring with colour scheme
+ rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+ shader = new ResidueShader(new ZappoColourScheme());
+
+ // M residue pink
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.pink, c);
+
+ // gaps blue
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.blue, c);
+
+ // legacy colouring with colour scheme
+ rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+
+ // M residue pink
+ c = rcf.getBoxColour(shader, seq, 0);
+ assertEquals(Color.pink, c);
+
+ // gaps white
+ c = rcf.getBoxColour(shader, seq, 3);
+ assertEquals(Color.white, c);
+ }
+}
--- /dev/null
+/*
+ * 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.renderer;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+import java.awt.Color;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ResidueColourFinderTest
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueColour_zappo()
+ {
+ SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new ResidueColourFinder();
+ av.setGlobalColourScheme(new ZappoColourScheme());
+
+ // @see ResidueProperties.zappo
+ assertEquals(Color.pink,
+ rcf.getResidueColour(true, av.getResidueShading(), null, seq, 0,
+ null)); // M
+ assertEquals(Color.green,
+ rcf.getResidueColour(true, av.getResidueShading(), null, seq, 2,
+ null)); // T
+ assertEquals(Color.magenta,
+ rcf.getResidueColour(true, av.getResidueShading(), null, seq, 5,
+ null)); // G
+ assertEquals(Color.orange,
+ rcf.getResidueColour(true, av.getResidueShading(), null, seq,
+ 12,
+ null)); // F
+
+ // everything is white if showBoxes is false
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 12, null)); // F
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueColour_none()
+ {
+ SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new ResidueColourFinder();
+
+ assertEquals(Color.white,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 0, null));
+ assertEquals(Color.white,
+ rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 2, null));
+
+ // no change if showBoxes is false
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 2, null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetResidueColour_userdef()
+ {
+ SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
+ // gap
+ AlignmentI al = new Alignment(new SequenceI[] { seq });
+ final AlignViewport av = new AlignViewport(al);
+ ResidueColourFinder rcf = new ResidueColourFinder();
+
+ Color[] newColours = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = null;
+ }
+
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour not specified so gap colour is null
+ // this is consistent with previous behaviour, but may not be correct?
+ assertEquals(null, rcf.getResidueColour(true, av.getResidueShading(),
+ null, seq, 3, null));
+
+ newColours[23] = Color.pink;
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour specified as pink
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(),
+ null, seq, 3, null));
+
+ // everything is white if showBoxes is false
+ newColours[23] = null;
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(),
+ null, seq, 3, null));
+
+ newColours[23] = Color.pink;
+ av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+ // gap colour specified as pink
+ assertEquals(Color.white, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
+ }
+
+ // TODO more tests for getResidueColour covering groups, feature rendering...
+}
git://source.jalview.org / jalview.git / commitdiff