minor changes, noted license change on website

Author: dfsp-spirit

plcc/doc/RELEASE_LOG

@@ -123,6 +123,7 @@ Updates from version 2012-10-11 to 2013-03-25:
 
 Updates from version 2013-03-25 to 2015-01-20:
 ================================================
+* ALL: license changed to GPL 2.0
 * PLCC
   - tons of changes and fixes, the code base may have doubled. some are given in the following list, more are forgotten already.
   - support for computing folding graphs (connected components of protein graphs)

plcc/src/plcc/ComplexGraph.java

@@ -66,7 +66,7 @@ public Vertex getVertexFromChain(String chainID) {
 
     public String getPDBID() {
         return this.pdbid;
-    }
+    }        
 
     /**
      * Writes this complex graph to the file 'file' in GML format. Note that

plcc/src/plcc/SSEGraph.java

@@ -32,6 +32,7 @@
 import java.awt.geom.AffineTransform;
 import java.awt.geom.Arc2D;
 import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
 import java.awt.geom.Line2D;
 import java.awt.geom.Rectangle2D;
 import java.awt.image.BufferedImage;
@@ -4003,6 +4004,7 @@ protected static ArrayList<Shape> getCrossoverArcConnectorAlternativeBezierVersi
         Integer downwards = 180;
 
         ArrayList<Shape> parts = new ArrayList<Shape>();
+        ArrayList<Shape> partsPath = new ArrayList<Shape>();
         Integer leftVertPosX, rightVertPosX, bothArcsXDistance, bothArcsSumHeight, vertStartY, leftArcHeight, leftArcWidth, rightArcHeight, rightArcWidth, arcWidth, arcEllipseHeight;
         Integer leftArcUpperLeftX, leftArcUpperLeftY, centerBetweenBothArcsX, centerBetweenBothArcsY, leftArcEndX, leftArcEndY, rightArcEndX, rightArcEndY;
         Integer leftArcLowerRightX, leftArcLowerRightY, leftArcUpperRightX, leftArcUpperRightY;
@@ -4046,6 +4048,8 @@ protected static ArrayList<Shape> getCrossoverArcConnectorAlternativeBezierVersi
 
         // everything computed, now start to create the shapes based on the required arc starting angle (up or down)
         Shape shape; Arc2D arc;
+        GeneralPath path = new GeneralPath();
+        path.moveTo(startX, startY);
 
         // TODO: we could draw these arcs using Quadratic and Cubic Curves (QuadCurve2D and CubicCurve2D).
         //       See the docs at http://docs.oracle.com/javase/tutorial/2d/overview/primitives.html for examples.
@@ -4061,6 +4065,7 @@ protected static ArrayList<Shape> getCrossoverArcConnectorAlternativeBezierVersi
             shape = stroke.createStrokedShape(arc);
             parts.add(shape);
 
+            path.curveTo(startX, (startY - leftArcHeight), leftArcEndX, (leftArcEndY - leftArcHeight), leftArcEndX, leftArcEndY);
 
             rightArcUpperLeftX = rightVertPosX - rightArcWidth;
             rightArcUpperLeftY = targetY;
@@ -4111,7 +4116,8 @@ protected static ArrayList<Shape> getCrossoverArcConnectorAlternativeBezierVersi
             parts.add(shape);
 
         }
-        return(parts);
+        return new ArrayList<>(partsPath);
+        //return(parts);
     }
 
 

plcc/website/index.html

@@ -42,7 +42,7 @@
 <p class="text">This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 <br />
 <br />
-VPLG is licensed under the <a href="http://www.perlfoundation.org/artistic_license_2_0" target="_blank">Artistic License 2.0</a>. This is a <a href="http://www.gnu.org/licenses/license-list.html%23ArtisticLicense2">free software license which is compatible with the GPL according to the FSF</a>. It is the same license that is used by the Perl programming language.
+VPLG is licensed under the <a href="http://www.gnu.org/licenses/gpl.html" target="_blank">GNU Public License 2.0</a>.
 <br />
 <br />
 Also keep in mind that the software is work in progress. You can download different versions, but it is recommended to always use the latest version.<br />