Revision: 21481
http://sourceforge.net/p/jmol/code/21481
Author: hansonr
Date: 2017-04-04 16:44:00 +0000 (Tue, 04 Apr 2017)
Log Message:
-----------
DSSR color NUCLEIC fixes adding "P" as gray
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/dssx/DSSR1.java
trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java
trunk/Jmol/src/org/jmol/util/ColorEncoder.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.java
Modified: trunk/Jmol/src/org/jmol/dssx/DSSR1.java
===================================================================
--- trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-04-04 15:44:44 UTC (rev
21480)
+++ trunk/Jmol/src/org/jmol/dssx/DSSR1.java 2017-04-04 16:44:00 UTC (rev
21481)
@@ -448,7 +448,7 @@
int pt = bs.nextSetBit(0);
if (pt < 0)
continue;
- if (Character.isLowerCase(ch))
+ if ("ACGTU".indexOf(ch) < 0)
atoms[pt].group.group1 = ch;
atoms[pt].group.dssrNT = map;
bs.clearAll();
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java 2017-04-04
15:44:44 UTC (rev 21480)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioResolver.java 2017-04-04
16:44:00 UTC (rev 21481)
@@ -1477,6 +1477,7 @@
private final static int[] argbsNucleic = {
0xFFBEA06E, // default tan
+ 0xFFA0A0A0, // grey P
0xFF0F820F, // green G
0xFFE6E600, // yellow C
0xFFE60A0A, // brightRed A
Modified: trunk/Jmol/src/org/jmol/util/ColorEncoder.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ColorEncoder.java 2017-04-04 15:44:44 UTC
(rev 21480)
+++ trunk/Jmol/src/org/jmol/util/ColorEncoder.java 2017-04-04 16:44:00 UTC
(rev 21481)
@@ -515,7 +515,7 @@
case AMINO:
return ce.getAmino()[colorIndex(val, n)];
case NUCLEIC:
- return ce.getNucleic()[colorIndex(val + 1 - JC.GROUPID_AMINO_MAX, n)];
+ return ce.getNucleic()[colorIndex(val - JC.GROUPID_AMINO_MAX + 2, n)];
case FRIENDLY:
return getPaletteAC()[colorIndexRepeat(val, n)];
default:
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2017-04-04 15:44:44 UTC
(rev 21480)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2017-04-04 16:44:00 UTC
(rev 21481)
@@ -134,8 +134,8 @@
// we need to use the byte form here for speed
switch (pid) {
case PAL.PALETTE_PROPERTY:
- return (colorData == null || atom.i >= colorData.length ? C.GRAY
- : ce.getColorIndex(colorData[atom.i]));
+ return (colorData == null || atom.i >= colorData.length ? C.GRAY : ce
+ .getColorIndex(colorData[atom.i]));
case PAL.PALETTE_NONE:
case PAL.PALETTE_CPK:
// Note that CPK colors can be changed based upon user preference
@@ -169,29 +169,28 @@
lo = 0;
hi = 100 * 100; // scaled by 100
}
- return ce.getColorIndexFromPalette(
- atom.getBfactor100(), lo, hi, ColorEncoder.BWR, false);
+ return ce.getColorIndexFromPalette(atom.getBfactor100(), lo, hi,
+ ColorEncoder.BWR, false);
case PAL.PALETTE_STRAIGHTNESS:
return ce.getColorIndexFromPalette(
- atom.group.getGroupParameter(T.straightness), -1, 1,
ColorEncoder.BWR,
- false);
+ atom.group.getGroupParameter(T.straightness), -1, 1,
+ ColorEncoder.BWR, false);
case PAL.PALETTE_SURFACE:
hi = vwr.ms.getSurfaceDistanceMax();
- return ce.getColorIndexFromPalette(
- atom.getSurfaceDistance100(), 0, hi, ColorEncoder.BWR, false);
+ return ce.getColorIndexFromPalette(atom.getSurfaceDistance100(), 0, hi,
+ ColorEncoder.BWR, false);
case PAL.PALETTE_NUCLEIC:
id = atom.group.groupID;
- if (id >= JC.GROUPID_NUCLEIC_MAX) {
- id = JC.GROUPID_AMINO_MAX +
"GCATUI".indexOf(Character.toUpperCase(atom.group.group1));
- }
- return ce.getColorIndexFromPalette(id,
- 0, 0, ColorEncoder.NUCLEIC, false);
+ if (id >= JC.GROUPID_NUCLEIC_MAX)
+ id = JC.GROUPID_AMINO_MAX
+ + "PGCATU".indexOf(Character.toUpperCase(atom.group.group1)) - 1;
+ return ce.getColorIndexFromPalette(id, 0, 0, ColorEncoder.NUCLEIC,
false);
case PAL.PALETTE_AMINO:
- return ce.getColorIndexFromPalette(atom.group.groupID,
- 0, 0, ColorEncoder.AMINO, false);
+ return ce.getColorIndexFromPalette(atom.group.groupID, 0, 0,
+ ColorEncoder.AMINO, false);
case PAL.PALETTE_SHAPELY:
- return ce.getColorIndexFromPalette(atom.group.groupID,
- 0, 0, ColorEncoder.SHAPELY, false);
+ return ce.getColorIndexFromPalette(atom.group.groupID, 0, 0,
+ ColorEncoder.SHAPELY, false);
case PAL.PALETTE_GROUP:
// vwr.calcSelectedGroupsCount() must be called first ...
// before we call getSelectedGroupCountWithinChain()
@@ -199,34 +198,30 @@
// however, do not call it here because it will get recalculated
// for each atom
// therefore, we call it in Eval.colorObject();
- return ce.getColorIndexFromPalette(
- atom.group.selectedIndex, 0,
- atom.group.chain.selectedGroupCount - 1, ColorEncoder.BGYOR,
- false);
+ return ce.getColorIndexFromPalette(atom.group.selectedIndex, 0,
+ atom.group.chain.selectedGroupCount - 1, ColorEncoder.BGYOR, false);
case PAL.PALETTE_POLYMER:
Model m = vwr.ms.am[atom.mi];
return ce.getColorIndexFromPalette(
- atom.group.getBioPolymerIndexInModel(), 0, (m.isBioModel ?
- ((BioModel) m).getBioPolymerCount() : 0) - 1,
+ atom.group.getBioPolymerIndexInModel(), 0,
+ (m.isBioModel ? ((BioModel) m).getBioPolymerCount() : 0) - 1,
ColorEncoder.BGYOR, false);
case PAL.PALETTE_MONOMER:
// vwr.calcSelectedMonomersCount() must be called first ...
- return ce.getColorIndexFromPalette(
- atom.group.getSelectedMonomerIndex(), 0,
- atom.group.getSelectedMonomerCount() - 1, ColorEncoder.BGYOR,
+ return ce.getColorIndexFromPalette(atom.group.getSelectedMonomerIndex(),
+ 0, atom.group.getSelectedMonomerCount() - 1, ColorEncoder.BGYOR,
false);
case PAL.PALETTE_MOLECULE:
return ce.getColorIndexFromPalette(
modelSet.getMoleculeIndex(atom.i, true), 0,
- modelSet.getMoleculeCountInModel(atom.mi) - 1,
- ColorEncoder.ROYGB, false);
+ modelSet.getMoleculeCountInModel(atom.mi) - 1, ColorEncoder.ROYGB,
+ false);
case PAL.PALETTE_ALTLOC:
//very inefficient!
modelIndex = atom.mi;
return ce
.getColorIndexFromPalette(
- modelSet.getAltLocIndexInModel(modelIndex,
- atom.altloc), 0,
+ modelSet.getAltLocIndexInModel(modelIndex, atom.altloc), 0,
modelSet.getAltLocCountInModel(modelIndex), ColorEncoder.ROYGB,
false);
case PAL.PALETTE_INSERTION:
@@ -256,7 +251,8 @@
}
chain = ((chain < 0 ? 0 : chain >= 256 ? chain - 256 : chain) & 0x1F)
% ColorEncoder.argbsChainAtom.length;
- argb = (atom.isHetero() ? ColorEncoder.argbsChainHetero :
ColorEncoder.argbsChainAtom)[chain];
+ argb = (atom.isHetero() ? ColorEncoder.argbsChainHetero
+ : ColorEncoder.argbsChainAtom)[chain];
break;
}
return (argb == 0 ? C.HOTPINK : C.getColix(argb));
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