diff --git a/uk/ac/sanger/artemis/components/BasePlot.java b/uk/ac/sanger/artemis/components/BasePlot.java
index 362c9efdd88aebc63853edf5cd46a2d061d3653f..5f0d00c21924ad1e75734e0c0f1f20d4f53975fc 100644
--- a/uk/ac/sanger/artemis/components/BasePlot.java
+++ b/uk/ac/sanger/artemis/components/BasePlot.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/BasePlot.java,v 1.19 2009-07-16 14:17:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/BasePlot.java,v 1.20 2009-07-20 15:11:17 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -54,7 +54,7 @@ import org.apache.log4j.Level;
* scale is tied to a FeatureDisplay component.
*
* @author Kim Rutherford
- * @version $Id: BasePlot.java,v 1.19 2009-07-16 14:17:11 tjc Exp $
+ * @version $Id: BasePlot.java,v 1.20 2009-07-20 15:11:17 tjc Exp $
**/
public class BasePlot extends Plot
@@ -739,10 +739,16 @@ public class BasePlot extends Plot
final int number_of_values = value_array_array[0].length;
boolean isWiggle = false;
+ boolean isBlast = false;
if(getAlgorithm() instanceof UserDataAlgorithm)
{
- if( ((UserDataAlgorithm)getAlgorithm()).wiggle != null )
+ int format = ((UserDataAlgorithm)getAlgorithm()).FORMAT;
+ if(format == UserDataAlgorithm.WIGGLE_FIXED_STEP_FORMAT ||
+ format == UserDataAlgorithm.WIGGLE_VARIABLE_STEP_FORMAT)
isWiggle = true;
+
+ if(format == UserDataAlgorithm.BLAST_FORMAT)
+ isBlast = true;
}
if(number_of_values > 1 && !isWiggle)
@@ -771,7 +777,7 @@ public class BasePlot extends Plot
getWidthInBases(),
offset,
value_array_array[value_index], value_index,
- get_values_return_count, isWiggle);
+ get_values_return_count, isWiggle, isBlast);
}
((Graphics2D)g).setStroke(stroke);
diff --git a/uk/ac/sanger/artemis/components/FeaturePlot.java b/uk/ac/sanger/artemis/components/FeaturePlot.java
index 112c90ee38d0742efe21d4e8349a23d697940abf..646f45c368a9789ed1a739fe710bb5d12dd82a7e 100644
--- a/uk/ac/sanger/artemis/components/FeaturePlot.java
+++ b/uk/ac/sanger/artemis/components/FeaturePlot.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeaturePlot.java,v 1.10 2009-07-16 14:17:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeaturePlot.java,v 1.11 2009-07-20 15:11:17 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -38,7 +38,7 @@ import java.awt.*;
* particular feature.
*
* @author Kim Rutherford
- * @version $Id: FeaturePlot.java,v 1.10 2009-07-16 14:17:11 tjc Exp $
+ * @version $Id: FeaturePlot.java,v 1.11 2009-07-20 15:11:17 tjc Exp $
**/
public class FeaturePlot extends Plot
@@ -330,7 +330,7 @@ public class FeaturePlot extends Plot
getSize ().width,
0, // no offset.
value_array_array[value_index], value_index,
- get_values_return_count, false);
+ get_values_return_count, false, false);
}
drawMinMax (g, min_value, max_value);
diff --git a/uk/ac/sanger/artemis/components/Plot.java b/uk/ac/sanger/artemis/components/Plot.java
index 3f1e4333e47c990854ed88be0ec161f3ca1c6bf8..fd897a3a633eb7e263653499aa95561050c7bf71 100644
--- a/uk/ac/sanger/artemis/components/Plot.java
+++ b/uk/ac/sanger/artemis/components/Plot.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/Plot.java,v 1.24 2009-07-16 14:17:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/Plot.java,v 1.25 2009-07-20 15:11:17 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -48,7 +48,7 @@ import javax.swing.JPopupMenu;
* This class implements a simple plot component.
*
* @author Kim Rutherford
- * @version $Id: Plot.java,v 1.24 2009-07-16 14:17:11 tjc Exp $
+ * @version $Id: Plot.java,v 1.25 2009-07-20 15:11:17 tjc Exp $
**/
public abstract class Plot extends JPanel
@@ -810,7 +810,8 @@ public abstract class Plot extends JPanel
final float [] plot_values,
final int value_index,
final int numberPlots,
- final boolean isWiggle)
+ final boolean isWiggle,
+ final boolean isBlast)
{
final float residues_per_pixel =
(float) total_unit_count / getSize().width;
@@ -848,8 +849,11 @@ public abstract class Plot extends JPanel
for(int i = 0; i<number_of_values - 1; ++i)
{
- if(isWiggle && plot_values[i] == 0)
- continue;
+ if( (isBlast || isWiggle) && plot_values[i] == 0)
+ {
+ if( !(isBlast && plotType.equals(LineAttributes.PLOT_TYPES[0])) )
+ continue;
+ }
start_residue = window_size / 2 + i * step_size + start_position;
start_x = (int)(start_residue / residues_per_pixel);
@@ -937,18 +941,18 @@ public abstract class Plot extends JPanel
float scale = ((float)(NUMBER_OF_SHADES-i) * (float)(255 / NUMBER_OF_SHADES )) ;
- if((R+scale) < 253)
+ if((R+scale) < 254)
R += scale;
else
- R = 253;
- if((G+scale) < 253)
+ R = 254;
+ if((G+scale) < 254)
G += scale;
else
- G = 253;
- if((B+scale) < 253)
+ G = 254;
+ if((B+scale) < 254)
B += scale;
else
- B = 253;
+ B = 254;
definedColour[i] = new Color(R,G,B);
}
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index dd9d71618e57387172fa36e3600bbe530cef5fa6..a501743c6b79a1f9e75b5f0d5b8044a193d9c683 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.11 2009-07-16 14:14:32 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.12 2009-07-20 15:11:18 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -31,10 +31,16 @@ import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.ReadFormatException;
import java.awt.Color;
+import java.awt.GridLayout;
import java.io.*;
import java.util.HashMap;
import java.util.regex.Pattern;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBox;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
/**
* Objects of this class have one useful method - getValues (), which takes a
* range of bases and returns a single floating point number. The number is
@@ -42,20 +48,22 @@ import java.util.regex.Pattern;
* set in the constructor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: UserDataAlgorithm.java,v 1.11 2009-07-16 14:14:32 tjc Exp $
+ * @version $Id: UserDataAlgorithm.java,v 1.12 2009-07-20 15:11:18 tjc Exp $
**/
public class UserDataAlgorithm extends BaseAlgorithm
{
/** A base per line file format */
- private static int BASE_PER_LINE_FORMAT = 1;
+ public static int BASE_PER_LINE_FORMAT = 1;
/** Base position is specified in the first column file format */
- private static int BASE_SPECIFIED_FORMAT = 2;
+ public static int BASE_SPECIFIED_FORMAT = 2;
/** Wiggle format */
- private static int WIGGLE_VARIABLE_STEP_FORMAT = 3;
- private static int WIGGLE_FIXED_STEP_FORMAT = 4;
+ public static int WIGGLE_VARIABLE_STEP_FORMAT = 3;
+ public static int WIGGLE_FIXED_STEP_FORMAT = 4;
+
+ public static int BLAST_FORMAT = 5;
/** The data read by the constructor - for BASE_PER_LINE_FORMAT */
private float data[][] = null;
@@ -83,7 +91,7 @@ public class UserDataAlgorithm extends BaseAlgorithm
private boolean logTransform;
/** Format type for this instance */
- private int FORMAT = BASE_PER_LINE_FORMAT;
+ public int FORMAT = BASE_PER_LINE_FORMAT;
private LineAttributes lines[];
@@ -113,10 +121,16 @@ public class UserDataAlgorithm extends BaseAlgorithm
String first_line = pushback_reader.readLine ();
Pattern dataPattern = Pattern.compile("^\\s*([\\d\\.]+\\s*)+$");
+ Pattern blastPattern = Pattern.compile(
+ "^(\\S+\\t+){2}[\\d\\.]+\\t+(\\d+\\t+){7}\\S+\\t+(\\d+)$");
if(dataPattern.matcher(first_line).matches())
FORMAT = BASE_PER_LINE_FORMAT;
- else
+ else if(blastPattern.matcher(first_line).matches())
{
+ FORMAT = BLAST_FORMAT;
+ }
+ else
+ {
StringBuffer header = new StringBuffer(first_line+"\n");
while(!dataPattern.matcher(first_line).matches())
@@ -143,6 +157,8 @@ public class UserDataAlgorithm extends BaseAlgorithm
if(FORMAT == BASE_SPECIFIED_FORMAT ||
FORMAT == BASE_PER_LINE_FORMAT)
readData(pushback_reader);
+ else if(FORMAT == BLAST_FORMAT)
+ readBlast(pushback_reader);
else
readWiggle(pushback_reader);
pushback_reader.close();
@@ -322,6 +338,105 @@ public class UserDataAlgorithm extends BaseAlgorithm
default_window_size = 1;
}
+
+ /**
+ * Read all from buffered_reader into data.
+ **/
+ private void readBlast (final LinePushBackReader pushback_reader)
+ throws IOException
+ {
+ String line = null;
+ int count = 0;
+ int lineNum = 0;
+ final int seqLength = getStrand ().getSequenceLength ();
+ final Pattern patt = Pattern.compile("\\t+");
+
+ dataMap = new HashMap<Integer, Float[]>();
+ this.number_of_values = 1;
+ int coordIndexStart = 6;
+ int coordIndexEnd = 7;
+
+ while ((line = pushback_reader.readLine ()) != null)
+ {
+ String tokens[] = patt.split(line.trim());
+
+ if(lineNum == 0)
+ {
+ final JPanel message = new JPanel(new GridLayout(2,1));
+
+ JCheckBox query = new JCheckBox("Query "+tokens[0], true);
+ message.add(query);
+ JCheckBox subj = new JCheckBox("Subject "+tokens[1], false);
+ message.add(subj);
+ ButtonGroup group = new ButtonGroup();
+ group.add(query);
+ group.add(subj);
+
+ JOptionPane.showConfirmDialog(null, message,
+ "Use Coordinates From", JOptionPane.OK_OPTION);
+ if(subj.isSelected())
+ {
+ coordIndexStart = 8;
+ coordIndexEnd = 9;
+ }
+ }
+ lineNum++;
+
+ int startBase = Integer.parseInt(tokens[coordIndexStart]);
+ int endBase = Integer.parseInt(tokens[coordIndexEnd]);
+ float value = Float.parseFloat(tokens[11]);
+
+ int valueIndex = 0;
+ try
+ {
+ if(startBase > seqLength || endBase > seqLength)
+ throw new ReadFormatException (
+ "the location ("+startBase+".."+endBase+
+ ") is outside than the sequence length:\n"+line);
+
+ if(logTransform)
+ value = (float) Math.log(value+1);
+
+ if (value > data_max)
+ data_max = value;
+ if (value < data_min)
+ data_min = value;
+
+ if(startBase > endBase)
+ {
+ int tmpStart = startBase;
+ startBase = endBase;
+ endBase = tmpStart;
+ }
+
+ final Float valueArray[] = new Float[number_of_values];
+ for (int base = startBase; base <= endBase; base++)
+ {
+ if (dataMap.containsKey(base))
+ {
+ Float oldValues[] = dataMap.get(base);
+ if(oldValues[0] > value)
+ value = oldValues[0];
+ }
+
+ valueArray[number_of_values - 1] = value;
+ dataMap.put(base, valueArray);
+ count++;
+ }
+
+ average_value += value;
+ }
+ catch (NumberFormatException e)
+ {
+ throw new ReadFormatException ("cannot understand this number: " +
+ tokens[valueIndex] + " - " +e.getMessage ());
+ }
+ }
+
+ average_value = average_value/count;
+ default_window_size = 1;
+ }
+
/**
* Return the value of the function between a pair of bases.
* @param start The start base (included in the range).
@@ -343,7 +458,8 @@ public class UserDataAlgorithm extends BaseAlgorithm
if(FORMAT == BASE_SPECIFIED_FORMAT ||
FORMAT == WIGGLE_VARIABLE_STEP_FORMAT ||
- FORMAT == WIGGLE_FIXED_STEP_FORMAT)
+ FORMAT == WIGGLE_FIXED_STEP_FORMAT ||
+ FORMAT == BLAST_FORMAT)
{
for (int i = 0 ; i < value_count ; ++i)
{