Menu
▾
▴
[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Backbone.java,1.12,1.13 BackboneRenderer.java,1.8,1.9 Cartoon.java,1.19,1.20 CartoonRenderer.java,1.23,1.24 Mcps.java,1.16,1.17 McpsRenderer.java,1.4,1.5 Strands.java,1.18,1.19 StrandsRenderer.java,1.16,1.17 Trace.java,1.28,1.29 TraceRenderer.java,1.24,1.25
|
From: Miguel <mic...@us...> - 2004-05-01 22:56:19
|
Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18582/src/org/openscience/jmol/viewer/datamodel Modified Files: Backbone.java BackboneRenderer.java Cartoon.java CartoonRenderer.java Mcps.java McpsRenderer.java Strands.java StrandsRenderer.java Trace.java TraceRenderer.java Log Message: name changes Index: Backbone.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Backbone.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- Backbone.java 11 Apr 2004 20:57:20 -0000 1.12 +++ Backbone.java 1 May 2004 22:56:10 -0000 1.13 @@ -30,13 +30,13 @@ class Backbone extends Mcps { - Mcps.Chain allocateMcpsChain(PdbPolymer polymer) { - return new Chain(polymer); + Mcps.Mcpschain allocateMcpschain(PdbPolymer polymer) { + return new Bbchain(polymer); } - class Chain extends Mcps.Chain { + class Bbchain extends Mcps.Mcpschain { - Chain(PdbPolymer polymer) { + Bbchain(PdbPolymer polymer) { super(polymer, 1, 1500, 500); } Index: BackboneRenderer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/BackboneRenderer.java,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- BackboneRenderer.java 11 Apr 2004 20:57:20 -0000 1.8 +++ BackboneRenderer.java 1 May 2004 22:56:10 -0000 1.9 @@ -33,13 +33,13 @@ class BackboneRenderer extends McpsRenderer { - void renderMcpsChain(Mcps.Chain mcpgChain) { - renderTraceChain((Backbone.Chain)mcpgChain); + void renderMcpschain(Mcps.Mcpschain mcpschain) { + renderTraceChain((Backbone.Bbchain)mcpschain); } - void renderTraceChain(Backbone.Chain backboneChain) { - render1Chain(backboneChain.polymerCount, backboneChain.polymer.getAtomIndices(), - backboneChain.mads, backboneChain.colixes); + void renderTraceChain(Backbone.Bbchain bbchain) { + render1Chain(bbchain.polymerCount, bbchain.polymer.getAtomIndices(), + bbchain.mads, bbchain.colixes); } void render1Chain(int polymerCount, int[] atomIndices, Index: Cartoon.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Cartoon.java,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- Cartoon.java 11 Apr 2004 20:57:20 -0000 1.19 +++ Cartoon.java 1 May 2004 22:56:10 -0000 1.20 @@ -31,13 +31,13 @@ class Cartoon extends Mcps { - Mcps.Chain allocateMcpsChain(PdbPolymer polymer) { - return new Chain(polymer); + Mcps.Mcpschain allocateMcpschain(PdbPolymer polymer) { + return new Cchain(polymer); } - class Chain extends Mcps.Chain { + class Cchain extends Mcps.Mcpschain { - Chain(PdbPolymer polymer) { + Cchain(PdbPolymer polymer) { super(polymer, -2, 3000, 500); } } Index: CartoonRenderer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/CartoonRenderer.java,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- CartoonRenderer.java 11 Apr 2004 20:57:20 -0000 1.23 +++ CartoonRenderer.java 1 May 2004 22:56:10 -0000 1.24 @@ -42,10 +42,9 @@ Cartoon cartoon; - void renderMcpsChain(Mcps.Chain mcpgChain) { - Cartoon.Chain cartoonChain = (Cartoon.Chain)mcpgChain; - render1Chain(cartoonChain.polymer, - cartoonChain.mads, cartoonChain.colixes); + void renderMcpschain(Mcps.Mcpschain mcpschain) { + Cartoon.Cchain cchain = (Cartoon.Cchain)mcpschain; + render1Chain(cchain.polymer, cchain.mads, cchain.colixes); } void render1Chain(PdbPolymer polymer, short[] mads, short[] colixes) { Index: Mcps.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Mcps.java,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- Mcps.java 11 Apr 2004 20:57:21 -0000 1.16 +++ Mcps.java 1 May 2004 22:56:10 -0000 1.17 @@ -37,7 +37,7 @@ PdbFile pdbFile; - Model[] models; + Mcpsmodel[] mcpsmodels; final void initShape() { pdbFile = frame.pdbFile; @@ -46,8 +46,8 @@ void setSize(int size, BitSet bsSelected) { short mad = (short) size; initialize(); - for (int m = models.length; --m >= 0; ) - models[m].setMad(mad, bsSelected); + for (int m = mcpsmodels.length; --m >= 0; ) + mcpsmodels[m].setMad(mad, bsSelected); } void setProperty(String propertyName, Object value, BitSet bs) { @@ -64,66 +64,66 @@ } else { return; } - for (int m = models.length; --m >= 0; ) - models[m].setColix(palette, colix, bs); + for (int m = mcpsmodels.length; --m >= 0; ) + mcpsmodels[m].setColix(palette, colix, bs); } - abstract Chain allocateMcpsChain(PdbPolymer polymer); + abstract Mcpschain allocateMcpschain(PdbPolymer polymer); void initialize() { - if (models == null) { + if (mcpsmodels == null) { int modelCount = pdbFile == null ? 0 : pdbFile.getModelCount(); - models = new Model[modelCount]; + mcpsmodels = new Mcpsmodel[modelCount]; for (int i = modelCount; --i >= 0; ) - models[i] = new Model(pdbFile.getModel(i)); + mcpsmodels[i] = new Mcpsmodel(pdbFile.getModel(i)); } } - int getModelCount() { - return models.length; + int getMcpsmodelCount() { + return mcpsmodels.length; } - Model getMcpsModel(int i) { - return models[i]; + Mcpsmodel getMcpsmodel(int i) { + return mcpsmodels[i]; } - class Model { - Chain[] chains; + class Mcpsmodel { + Mcpschain[] mcpschains; int modelNumber; - Model(PdbModel model) { - chains = new Chain[model.getChainCount()]; + Mcpsmodel(PdbModel model) { + mcpschains = new Mcpschain[model.getChainCount()]; this.modelNumber = model.getModelNumber(); - for (int i = chains.length; --i >= 0; ) - chains[i] = allocateMcpsChain(model.getChain(i).getPolymer()); + for (int i = mcpschains.length; --i >= 0; ) + mcpschains[i] = allocateMcpschain(model.getChain(i).getPolymer()); } void setMad(short mad, BitSet bsSelected) { - for (int i = chains.length; --i >= 0; ) { - Chain chain = chains[i]; + for (int i = mcpschains.length; --i >= 0; ) { + Mcpschain chain = mcpschains[i]; if (chain.polymerCount > 0) chain.setMad(mad, bsSelected); } } void setColix(byte palette, short colix, BitSet bsSelected) { - for (int i = chains.length; --i >= 0; ) { - Chain chain = chains[i]; + for (int i = mcpschains.length; --i >= 0; ) { + Mcpschain chain = mcpschains[i]; if (chain.polymerCount > 0) chain.setColix(palette, colix, bsSelected); } } - int getChainCount() { - return chains.length; + int getMcpschainCount() { + return mcpschains.length; } - Chain getMcpsChain(int i) { - return chains[i]; + Mcpschain getMcpschain(int i) { + return mcpschains[i]; } } - abstract class Chain { + abstract class Mcpschain { PdbPolymer polymer; short madOn; short madHelixSheet; @@ -134,7 +134,7 @@ short[] colixes; short[] mads; - Chain(PdbPolymer polymer, int madOn, int madHelixSheet, int madTurnRandom) { + Mcpschain(PdbPolymer polymer, int madOn, int madHelixSheet, int madTurnRandom) { this.polymer = polymer; this.madOn = (short)madOn; this.madHelixSheet = (short)madHelixSheet; Index: McpsRenderer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/McpsRenderer.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- McpsRenderer.java 11 Apr 2004 20:57:21 -0000 1.4 +++ McpsRenderer.java 1 May 2004 22:56:10 -0000 1.5 @@ -36,17 +36,17 @@ if (shape == null) return; Mcps mcps = (Mcps)shape; - for (int m = mcps.getModelCount(); --m >= 0; ) { - Mcps.Model model = mcps.getMcpsModel(m); - if (displayModel > 0 && displayModel != model.modelNumber) + for (int m = mcps.getMcpsmodelCount(); --m >= 0; ) { + Mcps.Mcpsmodel mcpsmodel = mcps.getMcpsmodel(m); + if (displayModel > 0 && displayModel != mcpsmodel.modelNumber) continue; - for (int c = model.getChainCount(); --c >= 0; ) { - Mcps.Chain mcpsChain = model.getMcpsChain(c); - if (mcpsChain.polymerCount >= 2) - renderMcpsChain(mcpsChain); + for (int c = mcpsmodel.getMcpschainCount(); --c >= 0; ) { + Mcps.Mcpschain mcpschain = mcpsmodel.getMcpschain(c); + if (mcpschain.polymerCount >= 2) + renderMcpschain(mcpschain); } } } - abstract void renderMcpsChain(Mcps.Chain mcpsChain); + abstract void renderMcpschain(Mcps.Mcpschain mcpschain); } Index: Strands.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Strands.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- Strands.java 11 Apr 2004 20:57:21 -0000 1.18 +++ Strands.java 1 May 2004 22:56:10 -0000 1.19 @@ -38,15 +38,15 @@ * http://sgce.cbse.uab.edu/carson/papers/ribbons86/ribbons86.html ****************************************************************/ - Mcps.Chain allocateMcpsChain(PdbPolymer polymer) { - return new Chain(polymer); + Mcps.Mcpschain allocateMcpschain(PdbPolymer polymer) { + return new Schain(polymer); } - class Chain extends Mcps.Chain { + class Schain extends Mcps.Mcpschain { Point3f[] centers; Vector3f[] vectors; - Chain(PdbPolymer polymer) { + Schain(PdbPolymer polymer) { super(polymer, -2, 1500, 500); if (polymerCount > 0) { centers = new Point3f[polymerCount + 1]; Index: StrandsRenderer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/StrandsRenderer.java,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- StrandsRenderer.java 11 Apr 2004 20:57:21 -0000 1.16 +++ StrandsRenderer.java 1 May 2004 22:56:10 -0000 1.17 @@ -61,21 +61,21 @@ float strandSeparation; float baseOffset; - void renderMcpsChain(Mcps.Chain mcpgChain) { - Strands.Chain strandsChain = (Strands.Chain)mcpgChain; - polymerCount = strandsChain.polymerCount; + void renderMcpschain(Mcps.Mcpschain mcpschain) { + Strands.Schain schain = (Strands.Schain)mcpschain; + polymerCount = schain.polymerCount; strandCount = viewer.getStrandsCount(); strandSeparation = (strandCount <= 1 ) ? 0 : 1f / (strandCount - 1); baseOffset = ((strandCount & 1) == 0) ? strandSeparation / 2 : strandSeparation; - render1Chain(strandsChain.polymerCount, - strandsChain.polymerGroups, - strandsChain.centers, - strandsChain.vectors, - strandsChain.mads, - strandsChain.colixes); + render1Chain(schain.polymerCount, + schain.polymerGroups, + schain.centers, + schain.vectors, + schain.mads, + schain.colixes); } Index: Trace.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Trace.java,v retrieving revision 1.28 retrieving revision 1.29 diff -u -r1.28 -r1.29 --- Trace.java 11 Apr 2004 20:57:21 -0000 1.28 +++ Trace.java 1 May 2004 22:56:10 -0000 1.29 @@ -30,12 +30,12 @@ class Trace extends Mcps { - Mcps.Chain allocateMcpsChain(PdbPolymer polymer) { - return new Chain(polymer); + Mcps.Mcpschain allocateMcpschain(PdbPolymer polymer) { + return new Tchain(polymer); } - class Chain extends Mcps.Chain { - Chain(PdbPolymer polymer) { + class Tchain extends Mcps.Mcpschain { + Tchain(PdbPolymer polymer) { super(polymer, 600, 1500, 500); } } Index: TraceRenderer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/TraceRenderer.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- TraceRenderer.java 11 Apr 2004 20:57:21 -0000 1.24 +++ TraceRenderer.java 1 May 2004 22:56:10 -0000 1.25 @@ -39,12 +39,12 @@ alphas = null; } - void renderMcpsChain(Mcps.Chain mcpgChain) { - Trace.Chain traceChain = (Trace.Chain)mcpgChain; - render1Chain(traceChain.polymerCount, - traceChain.polymerGroups, - traceChain.mads, - traceChain.colixes); + void renderMcpschain(Mcps.Mcpschain mcpschain) { + Trace.Tchain tchain = (Trace.Tchain)mcpschain; + render1Chain(tchain.polymerCount, + tchain.polymerGroups, + tchain.mads, + tchain.colixes); } Point3i[] screens; |