JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with...

diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index 72ff49e..9c5187b 100644 (file)
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -42,7 +42,7 @@ jetty-util-9.2.10.v20150310.jar
 jfreesvg-2.1.jar       GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/
 JGoogleAnalytics_0.3.jar       APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
 jhall.jar
-Jmol-14.31.53.jar      GPL/LGPLv2 built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/a6a2fb767e3fc2a73e72d926a11fd93a0e4c9f23 (excluded jspecview/application to compile)
+Jmol-15.2.69-NOLOG4J.jar       GPL/LGPLv2 Jmol.jar and JSMol dist built manually from commit https://github.com/BobHanson/Jmol-SwingJS/commit/789ec9f0792931c6a1cb9ba7e4a82d360372260c and subsequent removal of org/apache/log4j directory
 json_simple-1.1.jar    Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)
 jsoup-1.8.1.jar
 jsr311-api-1.1.1.jar

diff --git a/j8lib/Jmol-NO_LOG4J-14.31.53.jar b/j11lib/Jmol-15.2.69-NOLOG4J.jar
similarity index 61%
rename from j8lib/Jmol-NO_LOG4J-14.31.53.jar
rename to j11lib/Jmol-15.2.69-NOLOG4J.jar
index ff69d31..1336aa2 100644 (file)
Binary files a/j8lib/Jmol-NO_LOG4J-14.31.53.jar and b/j11lib/Jmol-15.2.69-NOLOG4J.jar differ

diff --git a/j11lib/Jmol-NO_LOG4J-14.31.53.jar b/j8lib/Jmol-15.2.69-NOLOG4J.jar
similarity index 61%
rename from j11lib/Jmol-NO_LOG4J-14.31.53.jar
rename to j8lib/Jmol-15.2.69-NOLOG4J.jar
index bc3c77f..1336aa2 100644 (file)
Binary files a/j11lib/Jmol-NO_LOG4J-14.31.53.jar and b/j8lib/Jmol-15.2.69-NOLOG4J.jar differ

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 895db9a..46e17ec 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -173,13 +173,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // //////////////////////////
 
   @Override
-  public float[][] functionXY(String functionName, int x, int y)
+  public double[][] functionXY(String functionName, int x, int y)
   {
     return null;
   }
 
   @Override
-  public float[][][] functionXYZ(String functionName, int nx, int ny,
+  public double[][][] functionXYZ(String functionName, int nx, int ny,
           int nz)
   {
     // TODO Auto-generated method stub

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ab6bbcc..45f3d7c 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,23 +20,11 @@
  */
 package jalview.ext.jmol;
 
-import java.util.Locale;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Format;
-import jalview.util.MessageManager;
-
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 
@@ -49,6 +37,16 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -662,7 +660,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public float[][] functionXY(String functionName, int x, int y)
+  public double[][] functionXY(String functionName, int x, int y)
   {
     return null;
   }
@@ -671,7 +669,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public float[][][] functionXYZ(String functionName, int nx, int ny,
+  public double[][][] functionXYZ(String functionName, int nx, int ny,
           int nz)
   {
     return null;

diff --git a/src/mc_view/AppletPDBCanvas.java b/src/mc_view/AppletPDBCanvas.java
index fe1aca1..768f1d6 100644 (file)
--- a/src/mc_view/AppletPDBCanvas.java
+++ b/src/mc_view/AppletPDBCanvas.java
@@ -20,21 +20,6 @@
  */
 package mc_view;
 
-import jalview.analysis.AlignSeq;
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.FeatureRenderer;
-import jalview.appletgui.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Event;
@@ -52,6 +37,21 @@ import java.io.PrintStream;
 import java.util.List;
 import java.util.Vector;
 
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
 public class AppletPDBCanvas extends Panel
         implements MouseListener, MouseMotionListener, StructureListener
 {
@@ -82,13 +82,13 @@ public class AppletPDBCanvas extends Panel
 
   Dimension prefsize;
 
-  float[] centre = new float[3];
+  double[] centre = new double[3];
 
-  float[] width = new float[3];
+  double[] width = new double[3];
 
-  float maxwidth;
+  double maxwidth;
 
-  float scale;
+  double scale;
 
   String inStr;
 
@@ -178,7 +178,7 @@ public class AppletPDBCanvas extends Panel
 
     colourBySequence();
 
-    float max = -10;
+    double max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -317,16 +317,16 @@ public class AppletPDBCanvas extends Panel
 
   public void findWidth()
   {
-    float[] max = new float[3];
-    float[] min = new float[3];
+    double[] max = new double[3];
+    double[] min = new double[3];
 
-    max[0] = (float) -1e30;
-    max[1] = (float) -1e30;
-    max[2] = (float) -1e30;
+    max[0] = -1e30;
+    max[1] = -1e30;
+    max[2] = -1e30;
 
-    min[0] = (float) 1e30;
-    min[1] = (float) 1e30;
-    min[2] = (float) 1e30;
+    min[0] = 1e30;
+    min[1] = 1e30;
+    min[2] = 1e30;
 
     for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
@@ -418,7 +418,7 @@ public class AppletPDBCanvas extends Panel
     // System.out.println("Maxwidth = " + maxwidth);
   }
 
-  public float findScale()
+  public double findScale()
   {
     int dim;
     int width;
@@ -444,14 +444,14 @@ public class AppletPDBCanvas extends Panel
       dim = height;
     }
 
-    return (float) (dim / (1.5d * maxwidth));
+    return dim / (1.5d * maxwidth);
   }
 
   public void findCentre()
   {
-    float xtot = 0;
-    float ytot = 0;
-    float ztot = 0;
+    double xtot = 0;
+    double ytot = 0;
+    double ztot = 0;
 
     int bsize = 0;
 
@@ -473,9 +473,9 @@ public class AppletPDBCanvas extends Panel
       }
     }
 
-    centre[0] = xtot / (2 * (float) bsize);
-    centre[1] = ytot / (2 * (float) bsize);
-    centre[2] = ztot / (2 * (float) bsize);
+    centre[0] = xtot / (2 * (double) bsize);
+    centre[1] = ytot / (2 * (double) bsize);
+    centre[2] = ztot / (2 * (double) bsize);
   }
 
   @Override
@@ -733,7 +733,7 @@ public class AppletPDBCanvas extends Panel
   {
     if (!wire)
     {
-      if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
+      if (((double) Math.abs(y2 - y1) / (double) Math.abs(x2 - x1)) < 0.5)
       {
         g.drawLine(x1, y1, x2, y2);
         g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
@@ -767,13 +767,13 @@ public class AppletPDBCanvas extends Panel
   {
     if (evt.getKeyCode() == KeyEvent.VK_UP)
     {
-      scale = (float) (scale * 1.1);
+      scale = scale * 1.1;
       redrawneeded = true;
       repaint();
     }
     else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
     {
-      scale = (float) (scale * 0.9);
+      scale = scale * 0.9;
       redrawneeded = true;
       repaint();
     }

diff --git a/src/mc_view/Atom.java b/src/mc_view/Atom.java
index 3b4f409..2416270 100755 (executable)
--- a/src/mc_view/Atom.java
+++ b/src/mc_view/Atom.java
@@ -20,17 +20,17 @@
  */
 package mc_view;
 
-import jalview.schemes.ResidueProperties;
-
 import java.awt.Color;
 
+import jalview.schemes.ResidueProperties;
+
 public class Atom
 {
-  public float x;
+  public double x;
 
-  public float y;
+  public double y;
 
-  public float z;
+  public double z;
 
   public int number;
 
@@ -60,9 +60,9 @@ public class Atom
 
   public int atomIndex;
 
-  public float occupancy = 0;
+  public double occupancy = 0;
 
-  public float tfactor = 0;
+  public double tfactor = 0;
 
   // need these if we ever want to export Atom data
   // public boolean tfacset=true,occset=true;
@@ -127,10 +127,10 @@ public class Atom
     return false;
   }
 
-  public Atom(float x, float y, float z)
+  public Atom(double x2, double y2, double z2)
   {
-    this.x = x;
-    this.y = y;
-    this.z = z;
+    this.x = x2;
+    this.y = y2;
+    this.z = z2;
   }
 }

diff --git a/src/mc_view/Bond.java b/src/mc_view/Bond.java
index e609506..0714ae3 100755 (executable)
--- a/src/mc_view/Bond.java
+++ b/src/mc_view/Bond.java
@@ -24,9 +24,9 @@ import java.awt.Color;
 
 public class Bond
 {
-  float[] start;
+  double[] start;
 
-  float[] end;
+  double[] end;
 
   Color startCol = Color.lightGray;
 
@@ -38,8 +38,8 @@ public class Bond
 
   public Bond(Atom at1, Atom at2)
   {
-    this.start = new float[] { at1.x, at1.y, at1.z };
-    this.end = new float[] { at2.x, at2.y, at2.z };
+    this.start = new double[] { at1.x, at1.y, at1.z };
+    this.end = new double[] { at2.x, at2.y, at2.z };
     this.startCol = at1.color;
     this.endCol = at2.color;
     this.at1 = at1;
@@ -68,7 +68,7 @@ public class Bond
    * return len; }
    */
 
-  public void translate(float x, float y, float z)
+  public void translate(double x, double y, double z)
   {
     start[0] = start[0] + x;
     end[0] = end[0] + x;

diff --git a/src/mc_view/MCMatrix.java b/src/mc_view/MCMatrix.java
index 01be1f9..61c46cc 100755 (executable)
--- a/src/mc_view/MCMatrix.java
+++ b/src/mc_view/MCMatrix.java
@@ -22,31 +22,31 @@ package mc_view;
 
 public class MCMatrix
 {
-  float[][] matrix;
+  double[][] matrix;
 
-  float[][] tmp;
+  double[][] tmp;
 
-  float mycos;
+  double mycos;
 
-  float mysin;
+  double mysin;
 
-  float myconst = (float) (Math.PI / 180);
+  double myconst = Math.PI / 180;
 
   public MCMatrix(int rows, int cols)
   {
-    matrix = new float[rows][cols];
-    tmp = new float[rows][cols];
+    matrix = new double[rows][cols];
+    tmp = new double[rows][cols];
   }
 
-  public void addElement(int i, int j, float value)
+  public void addElement(int i, int j, double value)
   {
     matrix[i][j] = value;
   }
 
-  public void rotatex(float degrees)
+  public void rotatex(double degrees)
   {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
+    mycos = (Math.cos(degrees * myconst));
+    mysin = (Math.sin(degrees * myconst));
 
     tmp[0][0] = 1;
     tmp[0][1] = 0;
@@ -60,10 +60,10 @@ public class MCMatrix
     preMultiply(tmp);
   }
 
-  public void rotatez(float degrees)
+  public void rotatez(double degrees)
   {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
+    mycos = (Math.cos(degrees * myconst));
+    mysin = (Math.sin(degrees * myconst));
 
     tmp[0][0] = mycos;
     tmp[0][1] = -mysin;
@@ -78,10 +78,10 @@ public class MCMatrix
     preMultiply(tmp);
   }
 
-  public void rotatey(float degrees)
+  public void rotatey(double degrees)
   {
-    mycos = (float) (Math.cos(degrees * myconst));
-    mysin = (float) (Math.sin(degrees * myconst));
+    mycos = (Math.cos(degrees * myconst));
+    mysin = (Math.sin(degrees * myconst));
 
     tmp[0][0] = mycos;
     tmp[0][1] = 0;
@@ -96,9 +96,9 @@ public class MCMatrix
     preMultiply(tmp);
   }
 
-  public float[] vectorMultiply(float[] vect)
+  public double[] vectorMultiply(double[] vect)
   {
-    float[] temp = new float[3];
+    double[] temp = new double[3];
 
     temp[0] = vect[0];
     temp[1] = vect[1];
@@ -106,9 +106,8 @@ public class MCMatrix
 
     for (int i = 0; i < 3; i++)
     {
-      temp[i] = ((float) matrix[i][0] * vect[0])
-              + ((float) matrix[i][1] * vect[1])
-              + ((float) matrix[i][2] * vect[2]);
+      temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+              + (matrix[i][2] * vect[2]);
     }
 
     vect[0] = temp[0];
@@ -118,9 +117,9 @@ public class MCMatrix
     return vect;
   }
 
-  public void preMultiply(float[][] mat)
+  public void preMultiply(double[][] mat)
   {
-    float[][] tmp = new float[3][3];
+    double[][] tmp = new double[3][3];
 
     for (int i = 0; i < 3; i++)
     {
@@ -140,9 +139,9 @@ public class MCMatrix
     }
   }
 
-  public void postMultiply(float[][] mat)
+  public void postMultiply(double[][] mat)
   {
-    float[][] tmp = new float[3][3];
+    double[][] tmp = new double[3][3];
 
     for (int i = 0; i < 3; i++)
     {

diff --git a/src/mc_view/PDBCanvas.java b/src/mc_view/PDBCanvas.java
index c15b54f..ca0b533 100644 (file)
--- a/src/mc_view/PDBCanvas.java
+++ b/src/mc_view/PDBCanvas.java
@@ -20,20 +20,6 @@
  */
 package mc_view;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Event;
@@ -55,6 +41,20 @@ import java.util.Vector;
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
 
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
 public class PDBCanvas extends JPanel
         implements MouseListener, MouseMotionListener, StructureListener
 {
@@ -80,13 +80,13 @@ public class PDBCanvas extends JPanel
 
   Dimension prefsize;
 
-  float[] centre = new float[3];
+  double[] centre = new double[3];
 
-  float[] width = new float[3];
+  double[] width = new double[3];
 
-  float maxwidth;
+  double maxwidth;
 
-  float scale;
+  double scale;
 
   String inStr;
 
@@ -298,8 +298,8 @@ public class PDBCanvas extends JPanel
 
   public void findWidth()
   {
-    float[] max = new float[3];
-    float[] min = new float[3];
+    double[] max = new double[3];
+    double[] min = new double[3];
 
     max[0] = (float) -1e30;
     max[1] = (float) -1e30;
@@ -433,9 +433,9 @@ public class PDBCanvas extends JPanel
 
   public void findCentre()
   {
-    float xtot = 0;
-    float ytot = 0;
-    float ztot = 0;
+    double xtot = 0;
+    double ytot = 0;
+    double ztot = 0;
 
     int bsize = 0;
 

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 72d276e..e854247 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -20,6 +20,11 @@
  */
 package mc_view;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Locale;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -33,11 +38,6 @@ import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Locale;
-import java.util.Vector;
-
 public class PDBChain
 {
   public static final String RESNUM_FEATURE = "RESNUM";
@@ -441,7 +441,7 @@ public class PDBChain
         SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
                 offset + count, offset + count, pdbid);
         resFeatures.addElement(sf);
-        resAnnotation.addElement(new Annotation(tmpat.tfactor));
+        resAnnotation.addElement(new Annotation((float) tmpat.tfactor));
         // Keep totting up the sequence
 
         if ((symbol = ResidueProperties.getAA3Hash()
@@ -694,8 +694,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq
-                .getEnd(), k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq.getEnd(),
+                k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);
 

diff --git a/src/mc_view/Zsort.java b/src/mc_view/Zsort.java
index a2080eb..96cd16b 100755 (executable)
--- a/src/mc_view/Zsort.java
+++ b/src/mc_view/Zsort.java
@@ -49,7 +49,7 @@ public class Zsort
 
   private int partition(Vector<Bond> bonds, int p, int r)
   {
-    float x = bonds.elementAt(p).start[2];
+    double x = bonds.elementAt(p).start[2];
     int i = p - 1;
     int j = r + 1;
     Bond tmp;

diff --git a/utils/jalviewjs/libjs/jmol-app.zip b/utils/jalviewjs/libjs/jmol-app.zip
index 65732a4..e864d3b 100644 (file)
Binary files a/utils/jalviewjs/libjs/jmol-app.zip and b/utils/jalviewjs/libjs/jmol-app.zip differ