import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
+import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.Platform;
import java.awt.BasicStroke;
import java.awt.Color;
import java.util.BitSet;
import java.util.Hashtable;
-import com.stevesoft.pat.Regex;
-
public class AnnotationRenderer
{
private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
*/
private final boolean debugRedraw;
+ private int charWidth, endRes, charHeight;
+
+ private boolean validCharWidth, hasHiddenColumns;
+
+ private FontMetrics fm;
+
+ private final boolean MAC = Platform.isAMac();
+
+ boolean av_renderHistogram = true, av_renderProfile = true,
+ av_normaliseProfile = false;
+
+ ResidueShaderI profcolour = null;
+
+ private ColumnSelection columnSelection;
+
+ private HiddenColumns hiddenColumns;
+
+ private ProfilesI hconsensus;
+
+ private Hashtable[] complementConsensus;
+
+ private Hashtable[] hStrucConsensus;
+
+ private boolean av_ignoreGapsConsensus;
+
+ /**
+ * attributes set from AwtRenderPanelI
+ */
+ /**
+ * old image used when data is currently being calculated and cannot be
+ * rendered
+ */
+ private Image fadedImage;
+
+ /**
+ * panel being rendered into
+ */
+ private ImageObserver annotationPanel;
+
+ /**
+ * width of image to render in panel
+ */
+ private int imgWidth;
+
+ /**
+ * offset to beginning of visible area
+ */
+ private int sOffset;
+
+ /**
+ * offset to end of visible area
+ */
+ private int visHeight;
+
+ /**
+ * indicate if the renderer should only render the visible portion of the
+ * annotation given the current view settings
+ */
+ private boolean useClip = true;
+
+ /**
+ * master flag indicating if renderer should ever try to clip. not enabled for
+ * jalview 2.8.1
+ */
+ private boolean canClip = false;
+
public AnnotationRenderer()
{
this(false);
this.debugRedraw = debugRedraw;
}
- public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ /**
+ * Remove any references and resources when this object is no longer required
+ */
+ public void dispose()
+ {
+ hconsensus = null;
+ complementConsensus = null;
+ hStrucConsensus = null;
+ fadedImage = null;
+ annotationPanel = null;
+ }
+
+ void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
+ int x, int y, int iconOffset, int startRes, int column,
+ boolean validRes, boolean validEnd)
{
g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
- Regex closeparen = new Regex("(\\))");
char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
: row_annotations[column - 1].secondaryStructure;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
- // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
- // If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
- {
+ if (column > 0 && Rna.isClosingParenthesis(dc))
+ {
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
+ /*
+ * if new annotation with a closing base pair half of the stem,
+ * display a backward arrow
+ */
g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[] { y + iconOffset, y + 14 + iconOffset,
y + 8 + iconOffset }, 3);
}
else
{
-
// display a forward arrow
if (diffdownstream)
{
+ /*
+ * if annotation ending with an opeing base pair half of the stem,
+ * display a forward arrow
+ */
g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
- private int charWidth, endRes, charHeight;
-
- private boolean validCharWidth, hasHiddenColumns;
-
- private FontMetrics fm;
-
- private final boolean MAC = jalview.util.Platform.isAMac();
-
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
-
- ColourSchemeI profcolour = null;
-
- private ColumnSelection columnSelection;
-
- private Hashtable[] hconsensus;
-
- private Hashtable[] complementConsensus;
-
- private Hashtable[] hStrucConsensus;
-
- private boolean av_ignoreGapsConsensus;
-
- /**
- * attributes set from AwtRenderPanelI
- */
- /**
- * old image used when data is currently being calculated and cannot be
- * rendered
- */
- private Image fadedImage;
-
- /**
- * panel being rendered into
- */
- private ImageObserver annotationPanel;
-
- /**
- * width of image to render in panel
- */
- private int imgWidth;
-
- /**
- * offset to beginning of visible area
- */
- private int sOffset;
-
- /**
- * offset to end of visible area
- */
- private int visHeight;
-
- /**
- * indicate if the renderer should only render the visible portion of the
- * annotation given the current view settings
- */
- private boolean useClip = true;
-
- /**
- * master flag indicating if renderer should ever try to clip. not enabled for
- * jalview 2.8.1
- */
- private boolean canClip = false;
-
- public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
Annotation[] row_annotations, int lastSSX, int x, int y,
int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
- Regex closeparen = new Regex("}|]|<|[a-z]");
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
|| !dc.equals(row_annotations[column].displayCharacter);
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
- // )
+ if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
- endRes = av.getEndRes();
+ endRes = av.getRanges().getEndRes();
charHeight = av.getCharHeight();
hasHiddenColumns = av.hasHiddenColumns();
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
av_normaliseProfile = av.isNormaliseSequenceLogo();
- profcolour = av.getGlobalColourScheme();
- if (profcolour == null)
+ profcolour = av.getResidueShading();
+ if (profcolour == null || profcolour.getColourScheme() == null)
{
- // Set the default colour for sequence logo if the alignnent has no
- // colourscheme set
- profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
- : new jalview.schemes.ZappoColourScheme();
+ /*
+ * Use default colour for sequence logo if
+ * the alignment has no colourscheme set
+ * (would like to use user preference but n/a for applet)
+ */
+ ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
+ : new ZappoColourScheme();
+ profcolour = new ResidueShader(col);
}
columnSelection = av.getColumnSelection();
+ hiddenColumns = av.getAlignment().getHiddenColumns();
hconsensus = av.getSequenceConsensusHash();
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
* @param column
* @return
*/
- public int[] getProfileFor(AlignmentAnnotation aa, int column)
+ int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column],
+ aa.groupRef.consensusData.get(column),
aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
}
else
{
- return AAFrequency.extractProfile(hconsensus[column],
+ return AAFrequency.extractProfile(
+hconsensus.get(column),
av_ignoreGapsConsensus);
}
}
{
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(startRes + x);
+ column = hiddenColumns.adjustForHiddenColumns(startRes + x);
if (column > row_annotations.length - 1)
{
break;
private Color sdNOTCANONICAL_COLOUR;
- public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
+ int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, Annotation[] row,
+ void drawSheetAnnot(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
}
- public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
+ int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
g.setColor(HELIX_COLOUR);
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
+ void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, int y,
float min, float max, int graphHeight)
{
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.adjustForHiddenColumns(column);
}
if (column > aaMax)
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+ void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
float max, int y, boolean renderHistogram, boolean renderProfile,
boolean normaliseProfile)
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.adjustForHiddenColumns(column);
}
if (column > aaMax)
scl = htn * scale * profl[c++];
lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
.getFontRenderContext());
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent())));
+ Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, scl / lm.getAscent()));
+ g.setFont(font);
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
// Debug - render boxes around characters
git://source.jalview.org / jalview.git / blobdiff