diff --git a/etc/versions b/etc/versions
index 72b839549e253da0c67ef8306edf4124e5a63bfe..93e4033bb8f9d4d8dcb245c9f9a9505431e3143d 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 14.2.5
-ACT Release 11.2.5
+Artemis Release 14.2.6
+ACT Release 11.2.6
DNAPlotter Release 1.9
BamView 1.2.8
diff --git a/lib/j2ssh/j2ssh.properties b/lib/j2ssh/j2ssh.properties
index ca0823e15bf4efea23a696f4913636b6df4d57e1..eeb9581e0228ff855ca2c05ece3e212bc9c7780d 100644
--- a/lib/j2ssh/j2ssh.properties
+++ b/lib/j2ssh/j2ssh.properties
@@ -54,7 +54,6 @@ default_db=%uniprot_bacteria
# remote directories to use as roots in the file manager
remotedir.PD=/nfs/pathdata
remotedir.PD2=/nfs/pathdata2
-remotedir.YP=/nfs/disk222/yeastpub
# local directories to use as roots in the file manager
localdir.PD=/nfs/pathdata
localdir.YP=/nfs/disk222/yeastpub
diff --git a/uk/ac/sanger/artemis/components/BasePlot.java b/uk/ac/sanger/artemis/components/BasePlot.java
index 1d46bfb497a598e6c9c28144bd353318685422a3..16e8e70b1e36dd0e1cad44f498988dfaa75b7a42 100644
--- a/uk/ac/sanger/artemis/components/BasePlot.java
+++ b/uk/ac/sanger/artemis/components/BasePlot.java
@@ -725,7 +725,7 @@ public class BasePlot extends Plot
if( getAlgorithm() instanceof UserDataAlgorithm &&
((UserDataAlgorithm)getAlgorithm()).FORMAT == UserDataAlgorithm.TABIX_INDEXED_FORMAT)
{
- ((UserDataAlgorithm) getAlgorithm()).readIndexValues(
+ ((UserDataAlgorithm) getAlgorithm()).readIndexValues(recalculate_flag,
entryGroup.getSequenceEntry(), getStart(), getEnd());
}
diff --git a/uk/ac/sanger/artemis/components/BasePlotGroup.java b/uk/ac/sanger/artemis/components/BasePlotGroup.java
index a17683a16cb749a6bd113ed57bb32064fbbb4554..759e613ff97c7e379ff42eaf8469b6bcf384360f 100644
--- a/uk/ac/sanger/artemis/components/BasePlotGroup.java
+++ b/uk/ac/sanger/artemis/components/BasePlotGroup.java
@@ -33,6 +33,7 @@ import java.awt.*;
import java.util.Vector;
import javax.swing.JComponent;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
/**
@@ -46,6 +47,8 @@ import javax.swing.JPanel;
public class BasePlotGroup extends JPanel
implements DisplayAdjustmentListener
{
+ private static final long serialVersionUID = 1L;
+
/**
* The EntryGroup that contains the sequence that this JComponent is
* displaying.
@@ -56,7 +59,7 @@ public class BasePlotGroup extends JPanel
* This array contains the Algorithm objects of the BasePlot components in
* this BasePlotGroup, as set by the constructor.
**/
- private final Vector plot_value_producers = new Vector ();
+ private final Vector<BaseAlgorithm> plot_value_producers = new Vector<BaseAlgorithm> ();
/**
* The layout object used by this component.
@@ -203,12 +206,40 @@ public class BasePlotGroup extends JPanel
**/
public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
{
+ final StringBuffer closingPlots = new StringBuffer();
final Component[] children = getComponents();
-
for(int i = 0 ; i<children.length ; ++i)
{
if(children[i] instanceof BasePlot)
+ {
+ // if this is an indexed sequence change hide any
+ // userplots that are not indexed
+ if(event.getType() == DisplayAdjustmentEvent.IDX_SEQUENCE_CHANGE)
+ {
+ Algorithm alg = ((BasePlot)children[i]).getAlgorithm();
+ if(alg instanceof UserDataAlgorithm &&
+ ((UserDataAlgorithm)alg).FORMAT != UserDataAlgorithm.TABIX_INDEXED_FORMAT &&
+ findPlotByAlgorithm(alg).isVisible())
+ {
+ closingPlots.append(alg.getAlgorithmName()+"\n");
+ setVisibleByAlgorithm(alg, false);
+ continue;
+ }
+ }
+
((BasePlot)children[i]).displayAdjustmentValueChanged(event);
+ }
+ }
+
+ if(event.getType() == DisplayAdjustmentEvent.IDX_SEQUENCE_CHANGE &&
+ closingPlots.length() > 0)
+ {
+ JOptionPane.showMessageDialog(this,
+ closingPlots.toString()+
+ "\nAs the sequence is changing the above user plots are closing as they are\n"+
+ "not indexed with multiple sequences. You can load in the correponding plot\n"+
+ "for the new sequence.",
+ "Closing Userplot", JOptionPane.INFORMATION_MESSAGE);
}
}
@@ -231,9 +262,7 @@ public class BasePlotGroup extends JPanel
{
for(int i = 0 ; i < plot_value_producers.size() ; ++i)
{
- final BaseAlgorithm this_algorithm =
- (BaseAlgorithm) plot_value_producers.elementAt(i);
-
+ final BaseAlgorithm this_algorithm = plot_value_producers.elementAt(i);
if(this_algorithm instanceof CodonUsageAlgorithm)
return (CodonUsageAlgorithm) this_algorithm;
}
@@ -252,8 +281,7 @@ public class BasePlotGroup extends JPanel
for(int i = 0 ; i < plot_value_producers.size () ; ++i)
{
- final BaseAlgorithm this_algorithm =
- (BaseAlgorithm) plot_value_producers.elementAt (i);
+ final BaseAlgorithm this_algorithm = plot_value_producers.elementAt (i);
return_array[i] = this_algorithm;
}
@@ -348,14 +376,6 @@ public class BasePlotGroup extends JPanel
return selection;
}
- /**
- * Return the EntryGroup object that was passed to the constructor.
- **/
- private EntryGroup getEntryGroup()
- {
- return entry_group;
- }
-
/**
* Return the GotoEventSource object that was passed to the constructor.
**/
diff --git a/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java b/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
index 223ea01638ad61b4206e8f02357745d2d6b0c169..911f0b74efbeb35c0972b12ce40815b73b8d60d3 100644
--- a/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
+++ b/uk/ac/sanger/artemis/components/DisplayAdjustmentEvent.java
@@ -100,6 +100,9 @@ public class DisplayAdjustmentEvent extends ChangeEvent
final static public int CONTIG_REV_COMP_EVENT = 4;
final static public int CONTIG_REORDER = 5;
+
+ /** change tabix indexed sequence */
+ final static public int IDX_SEQUENCE_CHANGE = 6;
public DisplayAdjustmentEvent(Object source,
int start_base, int end_base,
diff --git a/uk/ac/sanger/artemis/components/EntryGroupDisplay.java b/uk/ac/sanger/artemis/components/EntryGroupDisplay.java
index 426b11bf8c5e4ec44a25f1929b161bc58d26de0a..4cfc5f88d5ad530fc0c7187ef3fb5a7466e85155 100644
--- a/uk/ac/sanger/artemis/components/EntryGroupDisplay.java
+++ b/uk/ac/sanger/artemis/components/EntryGroupDisplay.java
@@ -251,6 +251,16 @@ public class EntryGroupDisplay extends JPanel
owning_component.getFeatureDisplay().getBases().clearCodonCache();
owning_component.getFeatureDisplay().needVisibleFeatureVectorUpdate();
owning_component.repaint();
+ owning_component.getBasePlotGroup().displayAdjustmentValueChanged(
+ new DisplayAdjustmentEvent(
+ owning_component,
+ owning_component.getFeatureDisplay().getFirstVisibleForwardBase(),
+ owning_component.getFeatureDisplay().getLastVisibleForwardBase(),
+ owning_component.getFeatureDisplay().getMaxVisibleBases(),
+ owning_component.getFeatureDisplay().getDisplayWidth(),
+ owning_component.getFeatureDisplay().getScaleFactor(),
+ owning_component.getFeatureDisplay().isRevCompDisplay(),
+ DisplayAdjustmentEvent.IDX_SEQUENCE_CHANGE));
}
};
}
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index a4e6fc83ee7ab1740b56d16eecc92a77a4a68e89..5813c61920aa31985ed937281a80731f256d79ac 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -835,11 +835,11 @@ public class UserDataAlgorithm extends BaseAlgorithm
return false;
}
- public void readIndexValues(Entry seqEntry, int start, int end)
+ public void readIndexValues(boolean recalculate_flag, Entry seqEntry, int start, int end)
{
if(start<1)
start = 1;
- idxReader.readValuesForRange(seqEntry, start, end);
+ idxReader.readValuesForRange(recalculate_flag, seqEntry, start, end);
}
class Wiggle
@@ -928,19 +928,21 @@ public class UserDataAlgorithm extends BaseAlgorithm
/**
* Read the values in a range
+ * @param recalculate_flag
* @param seqEntry - sequence entry
* @param start - start base
* @param end - end base
*/
- private void readValuesForRange(Entry seqEntry, int start, int end)
+ private void readValuesForRange(boolean recalculate_flag, Entry seqEntry, int start, int end)
{
- if(end <= start || (start == this.sbeg && end == this.send))
+ if(!recalculate_flag && (end <= start || (start == this.sbeg && end == this.send)) )
return;
this.sbeg = start;
this.send = end;
rvalues = new float[end-start+1][getNumberOfValues()];
final String r = getReferenceName(seqEntry)+":"+start+"-"+end;
+
try
{
final TabixReader.Iterator tbxIt = reader.query(r);