diff --git a/etc/versions b/etc/versions
index 1f22df39c3260e74eeb38d988df1b0a385f712e1..4527d9a3057c34d1903200f5298863478f742e56 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 14.2.0
-ACT Release 11.2.0
+Artemis Release 14.2.1
+ACT Release 11.2.1
DNAPlotter Release 1.8
-BamView 1.2.5
+BamView 1.2.6
diff --git a/uk/ac/sanger/artemis/components/Plot.java b/uk/ac/sanger/artemis/components/Plot.java
index 175832128117d16e0d85edf50e66e3b67e3f612a..9fcc723afc22fc2d14351ac2cb072652b0873014 100644
--- a/uk/ac/sanger/artemis/components/Plot.java
+++ b/uk/ac/sanger/artemis/components/Plot.java
@@ -938,8 +938,7 @@ public abstract class Plot extends JPanel
int R = col.getRed();
int G = col.getGreen();
int B = col.getBlue();
-
- float scale = ((float)(NUMBER_OF_SHADES-i) * (float)(255 / NUMBER_OF_SHADES )) ;
+ int scale = NUMBER_OF_SHADES-i;
if((R+scale) <= 255)
R += scale;
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index ca938c72d7d1b24bc0bf5e2212d81799faf0d407..654e724fc52d4f2544c550cbb043876cade1ea6f 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -216,6 +216,7 @@ public class BamView extends JPanel
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
+ private GroupBamFrame groupsFrame = new GroupBamFrame(this, bamFilesMenu);
private CoveragePanel coverageView = new CoveragePanel();
protected static String BAM_SUFFIX = ".*\\.(bam|cram)$";
@@ -372,6 +373,10 @@ public class BamView extends JPanel
public String getToolTipText()
{
+ if(isCoverageView(getPixPerBaseByWidth()) && lastMousePoint != null)
+ return coverageView.getToolTipText(
+ lastMousePoint.y-getJspView().getViewport().getViewPosition().y);
+
if(mouseOverSAMRecord == null)
return null;
@@ -677,7 +682,7 @@ public class BamView extends JPanel
final int cov[] = new int[nbins];
for(int i=0; i<nbins; i++)
cov[i] = 0;
-
+
final CloseableIterator<SAMRecord> it = inputSam.queryOverlapping(refName, start, end);
try
{
@@ -1809,7 +1814,7 @@ public class BamView extends JPanel
}
int hgt = jspView.getVisibleRect().height-scaleHeight;
- if(!cbCoverageStrandView.isSelected() && !cbCoverageHeatMap.isSelected())
+ if(!cbCoverageStrandView.isSelected() && !coverageView.isPlotHeatMap())
{
try
{
@@ -1824,8 +1829,9 @@ public class BamView extends JPanel
g2.translate(0, getJspView().getViewport().getViewPosition().y);
coverageView.drawSelectionRange(g2, pixPerBase, start, end, getHeight(), Color.PINK);
- coverageView.draw(g2, getWidth(), hgt);
- coverageView.drawMax(g2);
+ coverageView.draw(g2, getWidth(), hgt, hideBamList);
+ if(!coverageView.isPlotHeatMap())
+ coverageView.drawMax(g2);
}
/**
@@ -2408,9 +2414,8 @@ public class BamView extends JPanel
});
bamFilesMenu.setFont(addBam.getFont());
-
+
final JMenuItem groupBams = new JMenuItem("Group BAMs ...");
- final GroupBamFrame groupsFrame = new GroupBamFrame(this, bamFilesMenu);
groupBams.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent arg0)
{
@@ -3623,8 +3628,10 @@ public class BamView extends JPanel
*/
class PopupListener extends MouseAdapter
{
- JMenuItem gotoMateMenuItem;
- JMenuItem showDetails;
+ private JMenuItem gotoMateMenuItem;
+ private JMenuItem showDetails;
+ private JMenu coverageMenu;
+ private JMenuItem createGroup;
public void mouseClicked(MouseEvent e)
{
@@ -3637,7 +3644,13 @@ public class BamView extends JPanel
if(e.getClickCount() > 1)
getSelection().clear();
else if(e.getButton() == MouseEvent.BUTTON1)
- highlightSAMRecord = mouseOverSAMRecord;
+ {
+ if(isCoverageView(getPixPerBaseByWidth()))
+ coverageView.singleClick(e.isShiftDown(),
+ e.getPoint().y-getJspView().getViewport().getViewPosition().y);
+ else
+ highlightSAMRecord = mouseOverSAMRecord;
+ }
else
highlightRange(e, MouseEvent.BUTTON2_DOWN_MASK);
repaint();
@@ -3657,19 +3670,62 @@ public class BamView extends JPanel
private void maybeShowPopup(MouseEvent e)
{
if(e.isPopupTrigger())
- {
+ {
+ //
+ // main menu options
if(popup == null)
{
popup = new JPopupMenu();
createMenus(popup);
}
-
+
+ //
+ // coverage heatmap menu options
+ if(coverageMenu != null)
+ popup.remove(coverageMenu);
+ if(isCoverageView(getPixPerBaseByWidth()) && coverageView.isPlotHeatMap())
+ {
+ if(coverageMenu == null)
+ {
+ coverageMenu = new JMenu("Coverage HeatMap");
+ coverageView.createMenus(coverageMenu);
+
+ final JCheckBoxMenuItem coverageGrid = new JCheckBoxMenuItem("Show heatmap grid", false);
+ coverageGrid.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ coverageView.showLabels(coverageGrid.isSelected());
+ }
+ });
+ coverageMenu.add(coverageGrid);
+
+ createGroup = new JMenuItem("Create group from selected BAMs");
+ createGroup.addActionListener(new ActionListener()
+ {
+ private int n = 1;
+ public void actionPerformed(ActionEvent e)
+ {
+ String groupName = "group_"+n;
+ groupsFrame.addGroup(groupName);
+ final List<String> selected = coverageView.getSelected();
+ for(String sel: selected)
+ groupsFrame.addToGroup((new File(sel)).getName(), groupName);
+ groupsFrame.updateAndDisplay();
+ n++;
+ }
+ });
+ coverageMenu.add(createGroup);
+ }
+ createGroup.setEnabled(coverageView.hasSelectedBams());
+ popup.add(coverageMenu);
+ }
+
if(gotoMateMenuItem != null)
popup.remove(gotoMateMenuItem);
-
if(showDetails != null)
popup.remove(showDetails);
-
+
if( mouseOverSAMRecord != null &&
mouseOverSAMRecord.sam.getReadPairedFlag() &&
!mouseOverSAMRecord.sam.getMateUnmappedFlag() )
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 8942ad5e0f10097fd9a68965e2aaf71bde15d050..4810c54fbd65fc727e91a5c2e71feb95fa2ce1df 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -25,17 +25,21 @@
package uk.ac.sanger.artemis.components.alignment;
import java.awt.AlphaComposite;
+import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
+import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.geom.GeneralPath;
+import java.io.File;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
@@ -60,9 +64,12 @@ import net.sf.samtools.SAMRecord;
private static boolean redraw = false;
private boolean setMaxBases = false;
-
+
private boolean plotByStrand = false;
private boolean plotHeatMap = false;
+ private List<HeatMapLn> heatPlots;
+ private List<String> selected = new Vector<String>();
+ private boolean showGrid = false;
protected CoveragePanel(final BamView bamView)
{
@@ -180,7 +187,7 @@ import net.sf.samtools.SAMRecord;
}
}
- draw(g2, getWidth(), getHeight());
+ draw(g2, getWidth(), getHeight(), null);
}
protected void addRecord(SAMRecord thisRead, int offset, String fileName)
@@ -196,7 +203,7 @@ import net.sf.samtools.SAMRecord;
}
final int col;
- if(plotByStrand && thisRead.getReadNegativeStrandFlag())
+ if(plotByStrand && !isPlotHeatMap() && thisRead.getReadNegativeStrandFlag())
col = 1;
else
col = 0;
@@ -226,7 +233,7 @@ import net.sf.samtools.SAMRecord;
}
}
- protected void draw(Graphics2D g2, int wid, int hgt)
+ protected void draw(Graphics2D g2, int wid, int hgt, List<Short> hideBamList)
{
int size = bamView.bamList.size();
if(includeCombined)
@@ -237,35 +244,57 @@ import net.sf.samtools.SAMRecord;
else
lines = getLineAttributes(size);
-
+ if(plotHeatMap)
+ heatPlots = new Vector<HeatMapLn>();
Enumeration<String> plotEum = plots.keys();
while(plotEum.hasMoreElements())
{
- String fileName = (String) plotEum.nextElement();
- int[][] thisPlot = plots.get(fileName);
+ String fName = plotEum.nextElement();
+ int[][] thisPlot = plots.get(fName);
- int index;
- if(fileName.equals("-1"))
- index = lines.length-1;
+ int idx;
+ if(fName.equals("-1"))
+ idx = lines.length-1;
else
- index = bamView.bamList.indexOf(fileName);
+ idx = bamView.bamList.indexOf(fName);
+ final LineAttributes line = lines[idx];
if(plotHeatMap)
- drawHeatMap(g2, hgt, index, thisPlot);
+ {
+ if(hideBamList != null)
+ idx = adjustIdx(idx, hideBamList);
+ drawHeatMap(g2, hgt, line, idx, thisPlot, fName,
+ (idx == plots.size()-1));
+ }
else
- drawLinePlot(g2, wid, hgt, index, thisPlot);
+ drawLinePlot(g2, wid, hgt, line, thisPlot);
}
}
- private void drawLinePlot(final Graphics2D g2, int wid, int hgt, int index, int[][] thisPlot)
+ /**
+ * Adjust for BAM's that have been hidden
+ * @param index
+ * @param hideBamList
+ * @return
+ */
+ private int adjustIdx(int index, List<Short> hideBamList)
{
- g2.setColor(lines[index].getLineColour());
+ int shiftIdx = index;
+ for(short i=0; i<index; i++)
+ if(hideBamList.contains(i))
+ shiftIdx--;
+ return shiftIdx;
+ }
+
+ private void drawLinePlot(final Graphics2D g2, int wid, int hgt, LineAttributes line, int[][] thisPlot)
+ {
+ g2.setColor(line.getLineColour());
int hgt2 = hgt/2;
float maxVal = getValue(max);
- if(lines[index].getPlotType() == LineAttributes.PLOT_TYPES[0])
+ if(line.getPlotType() == LineAttributes.PLOT_TYPES[0])
{
- g2.setStroke(lines[index].getStroke());
+ g2.setStroke(line.getStroke());
for(int i=1; i<thisPlot.length; i++)
{
int x0 = (int) ((((i-1)*(windowSize)) + windowSize/2.f)*pixPerBase);
@@ -351,35 +380,52 @@ import net.sf.samtools.SAMRecord;
* Draw as heat map
* @param g2
* @param hgt
- * @param index
+ * @param line
+ * @param idx
* @param thisPlot
*/
- private void drawHeatMap(final Graphics2D g2, int hgt, int index, int[][] thisPlot)
+ private void drawHeatMap(final Graphics2D g2, int hgt, LineAttributes line, int idx, int[][] thisPlot, String fName, boolean lastPlot)
{ // heat map
- int NUMBER_OF_SHADES = 254;
- int plotHgt = hgt/plots.size();
- int plotPos = plotHgt * index;
- Color definedColours[] = Plot.makeColours(lines[index].getLineColour(),
- NUMBER_OF_SHADES);
+ final int NSHADES = 240;
+ final int plotHgt = hgt/plots.size();
+ final int plotPos = (hgt*idx)/plots.size();
+ final Color definedColours[] = Plot.makeColours(line.getLineColour(), NSHADES);
+
+ heatPlots.add(new HeatMapLn(plotPos, plotPos+plotHgt, fName));
float maxVal = getValue(max);
for(int i=0; i<thisPlot.length; i++)
{
int xpos = (int) (i*windowSize*pixPerBase);
-
// this is a number between 0.0 and 1.0
final float scaledValue = getValue(thisPlot[i][0]) / maxVal;
// set color based on value
- int colourIndex =
+ int colourIdx =
(int)(definedColours.length * 0.999 * scaledValue);
- if(colourIndex > definedColours.length - 1)
- colourIndex = definedColours.length - 1;
- else if (colourIndex < 0)
- colourIndex = 0;
-
- g2.setColor(definedColours[ colourIndex ]);
- g2.fillRect(xpos, plotPos, windowSize, plotHgt);
+ if(colourIdx > definedColours.length - 1)
+ colourIdx = definedColours.length - 1;
+ else if (colourIdx <= 0)
+ continue;
+
+ g2.setColor(definedColours[ colourIdx ]);
+ g2.fillRect(xpos, plotPos, (int) (windowSize*2*pixPerBase), plotHgt);
+ }
+
+ if(showGrid && !lastPlot)
+ {
+ g2.setColor(Color.darkGray);
+ g2.drawLine(0, plotPos+plotHgt-1, bamView.getWidth(), plotPos+plotHgt-1);
+ }
+
+ if(selected.contains(fName))
+ {
+ g2.setColor(Color.darkGray);
+ Stroke stroke = g2.getStroke();
+ g2.setStroke(new BasicStroke(2.f));
+ g2.drawLine(0, plotPos+1, bamView.getWidth(), plotPos+1);
+ g2.drawLine(0, plotPos+plotHgt-1, bamView.getWidth(), plotPos+plotHgt-1);
+ g2.setStroke(stroke);
}
}
@@ -433,6 +479,39 @@ import net.sf.samtools.SAMRecord;
this.plotHeatMap = plotHeatMap;
}
+ /**
+ * @return the plotHeatMap
+ */
+ protected boolean isPlotHeatMap()
+ {
+ return plotHeatMap;
+ }
+
+ /**
+ * Return tooltip text for a given position
+ * @param e
+ * @return
+ */
+ public String getToolTipText(int ypos)
+ {
+ if(heatPlots == null)
+ return null;
+ for(HeatMapLn h: heatPlots)
+ {
+ if(ypos > h.yTop && ypos < h.yBtm)
+ return h.toString();
+ }
+
+ return null;
+ }
+
+ protected void showLabels(boolean showLabel)
+ {
+ //
+ this.showGrid = showLabel;
+ bamView.repaint();
+ }
+
private void defineOpts()
{
final JPanel opts = new JPanel(new GridBagLayout());
@@ -509,5 +588,63 @@ import net.sf.samtools.SAMRecord;
return;
}
}
+
+ /**
+ * Click on heatmap
+ * @param y
+ */
+ protected void singleClick(boolean isShiftDown, int ypos)
+ {
+ if(!isPlotHeatMap())
+ return;
+
+ String sel = null;
+ for(HeatMapLn h: heatPlots)
+ {
+ if(ypos > h.yTop && ypos < h.yBtm)
+ sel = h.fName;
+ }
+
+ if(selected.contains(sel))
+ {
+ if(!isShiftDown)
+ selected.clear();
+ else
+ selected.remove(sel);
+ }
+ else
+ {
+ if(!isShiftDown)
+ selected.clear();
+ selected.add(sel);
+ }
+ }
+
+ protected boolean hasSelectedBams()
+ {
+ return (selected.size() > 0);
+ }
+
+ protected List<String> getSelected()
+ {
+ return selected;
+ }
+ class HeatMapLn
+ {
+ private int yTop, yBtm;
+ private String fName;
+ HeatMapLn(int yTop, int yBtm, String fName)
+ {
+ this.yTop = yTop;
+ this.yBtm = yBtm;
+ this.fName = fName;
+ }
+
+ public String toString()
+ {
+ final File f = new File(fName);
+ return f.getName();
+ }
+ }
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
index 148a80d90a4ed68ec98c554fea6bd47aa9e29caa..ee720fca2e79606505f59dc3b090db93c605fc19 100644
--- a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
@@ -66,7 +66,7 @@ class GroupBamFrame extends JFrame
newGroup.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
- addGroup(bamView, bamFilesMenu, newGroup, jsp);
+ addGroup(newGroup.getText().trim());
}
});
newGroup.addFocusListener(new java.awt.event.FocusAdapter() {
@@ -92,7 +92,7 @@ class GroupBamFrame extends JFrame
JOptionPane.INFORMATION_MESSAGE);
return;
}
- addGroup(bamView, bamFilesMenu, newGroup, jsp);
+ addGroup(newGroup.getText().trim());
}
});
xBox.add(Box.createHorizontalGlue());
@@ -148,18 +148,16 @@ class GroupBamFrame extends JFrame
setVisible(true);
}
- private void addGroup(final BamView bamView, final JMenu bamFilesMenu,
- final JTextField newGroup, final JScrollPane jsp)
+ protected void addGroup(final String newGroup)
{
final String tmpGroups[] = new String[groups.length+1];
- for(int i=0; i<groups.length; i++)
- tmpGroups[i] = groups[i];
- tmpGroups[tmpGroups.length-1] = newGroup.getText().trim();
+ System.arraycopy(groups, 0, tmpGroups, 0, groups.length);
+ tmpGroups[tmpGroups.length-1] = newGroup;
groups = tmpGroups;
updateGroupPanel();
updateBamPanel();
- jsp.validate();
+ validate();
}
private void updateBamPanel()
@@ -203,6 +201,29 @@ class GroupBamFrame extends JFrame
}
}
+ /**
+ * Add a BAM to a specified group
+ * @param bam
+ * @param group
+ */
+ protected void addToGroup(String bam, String group)
+ {
+ final Component cs[] = bamFilesMenu.getMenuComponents();
+ for(Component cp : cs)
+ {
+ if(cp instanceof JCheckBoxMenuItem)
+ {
+ final JCheckBoxMenuItem cbBam = (JCheckBoxMenuItem) cp;
+ final String thisBam = cbBam.getText();
+ if(bam.equals(thisBam))
+ {
+ bamGroupMap.get(cbBam).setSelectedItem(group);
+ return;
+ }
+ }
+ }
+ }
+
/**
* For a give BAM file return the group it belongs to.
* @param bamName
diff --git a/uk/ac/sanger/artemis/components/alignment/LineAttributes.java b/uk/ac/sanger/artemis/components/alignment/LineAttributes.java
index cb4cb0355d91c89ee485fb1df4e7844447989bd4..5030f576d8a1ea43a8769138a59d91d3e305602a 100644
--- a/uk/ac/sanger/artemis/components/alignment/LineAttributes.java
+++ b/uk/ac/sanger/artemis/components/alignment/LineAttributes.java
@@ -155,9 +155,9 @@ public class LineAttributes
new Color(0,200,0),
Color.blue,
Color.magenta,
- new Color(204, 204, 51),
- new Color(50, 255, 255),
- new Color(204, 51, 128),
+ new Color(100, 100, 0),
+ new Color(0, 100, 100),
+ new Color(50, 0, 50),
new Color(255, 102, 0),
Color.black };
final LineAttributes lines[] = new LineAttributes[numPlots];
diff --git a/uk/ac/sanger/artemis/io/RawStreamSequence.java b/uk/ac/sanger/artemis/io/RawStreamSequence.java
index 9337946b0887e3155348548d869b0d403a89de6b..1b6079c9cbc88ce01e8d743ecf4da83ed2e5fba6 100644
--- a/uk/ac/sanger/artemis/io/RawStreamSequence.java
+++ b/uk/ac/sanger/artemis/io/RawStreamSequence.java
@@ -25,6 +25,7 @@
package uk.ac.sanger.artemis.io;
+import uk.ac.sanger.artemis.sequence.BasePattern;
import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.IOException;
@@ -45,14 +46,14 @@ public class RawStreamSequence extends StreamSequence
* The _character_ positions of the header lines relative to the sequence.
* This is in the same order as fasta_header_strings.
**/
- private Vector fasta_header_positions = null;
+ private Vector<Integer> fasta_header_positions = null;
/**
* This Vector holds the fasta headers (if any) that where seen while
* reading the sequence. This is in the same order as
* fasta_header_positions.
**/
- private Vector fasta_header_strings = null;
+ private Vector<String> fasta_header_strings = null;
/**
* Create a new RawStreamSequence object from a stream containing raw
@@ -124,14 +125,14 @@ public class RawStreamSequence extends StreamSequence
* as it goes. No checks are made on the format of the sequence, apart
* from checking that the stream contains only letters.
**/
- protected void readSequence(final LinePushBackReader in_stream)
+ private void readSequence(final LinePushBackReader in_stream)
throws IOException
{
// initialise these here because this method is called before class
// variables are initialised
- fasta_header_positions = new Vector();
- fasta_header_strings = new Vector();
+ fasta_header_positions = new Vector<Integer>();
+ fasta_header_strings = new Vector<String>();
final int buffer_capacity = 5000;
@@ -141,29 +142,60 @@ public class RawStreamSequence extends StreamSequence
String line;
int nbase = 0;
+ boolean validSequenceCheck = true;
+ String hdrLine = null;
while((line = in_stream.readLine()) !=null)
{
if(line.startsWith(">"))
{
- final String header_string = line.substring(1);
- final Integer header_position = new Integer(nbase);
-
- fasta_header_strings.addElement(header_string);
- fasta_header_positions.addElement(header_position);
-
- // ignore header lines
+ storeHeader(line, nbase);
+ validSequenceCheck = true;
+ hdrLine = line;
continue;
}
line = line.trim().toLowerCase();
+
+ if(validSequenceCheck)
+ {
+ if(BasePattern.patternType(line) == BasePattern.ILLEGAL_PATTERN)
+ {
+ // ignore non-nucleotide sequence
+ if(hdrLine != null)
+ {
+ System.err.println(
+ "Warning:: ignore non-nucleotide sequence found in "+hdrLine.substring(1));
+ fasta_header_strings.remove(hdrLine.substring(1));
+ fasta_header_positions.remove(new Integer(nbase));
+ }
+
+ while((line = in_stream.readLine()) !=null)
+ {
+ if(line.startsWith(">"))
+ {
+ storeHeader(line, nbase);
+ hdrLine = line;
+ break;
+ }
+ }
+ continue;
+ }
+ validSequenceCheck = false;
+ }
if(line.length() > 0)
appendChar(line.toCharArray());
nbase += line.length();
+ hdrLine = null;
}
setCounts();
-
+ }
+
+ private void storeHeader(String line, int nbase)
+ {
+ fasta_header_strings.addElement(line.substring(1));
+ fasta_header_positions.addElement(new Integer(nbase));
}
/**
@@ -265,7 +297,7 @@ public class RawStreamSequence extends StreamSequence
if(fasta_header_positions != null && fasta_header_positions.size() > 0)
{
- Vector seen = new Vector(fasta_header_positions.size());
+ Vector<Integer> seen = new Vector<Integer>(fasta_header_positions.size());
for(int i = 0 ; i < fasta_header_positions.size(); ++i)
{
int current_position = ((Integer)fasta_header_positions.elementAt(i)).intValue();
diff --git a/uk/ac/sanger/artemis/sequence/BasePattern.java b/uk/ac/sanger/artemis/sequence/BasePattern.java
index df8006fe08a6ac4cb3c6c3e6226c7ff705f5e61f..86ea74fd283d68436245b915c79bd0ab0ca1c1a0 100644
--- a/uk/ac/sanger/artemis/sequence/BasePattern.java
+++ b/uk/ac/sanger/artemis/sequence/BasePattern.java
@@ -56,7 +56,7 @@ public class BasePattern {
/**
* A return value of patternType () - illegal characters in the pattern.
**/
- private static int ILLEGAL_PATTERN = -1;
+ public static int ILLEGAL_PATTERN = -1;
/**
* A return value of patternType () - the pattern contains only the
@@ -415,7 +415,7 @@ public class BasePattern {
* if the pattern contains only the characters a,t,g,c,r,y,k,m,s,w,n,b,d,h
* and v, ie IUC base codes.
**/
- private static int patternType (String pattern_string) {
+ public static int patternType (String pattern_string) {
boolean seen_iuc = false;
for (int i = 0 ; i < pattern_string.length () ; ++i) {