icn3d 3.25.8 → 3.25.9

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Files changed (4) hide show
  1. package/icn3d.js +41 -25
  2. package/icn3d.min.js +1 -1
  3. package/icn3d.module.js +41 -25
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -42024,18 +42024,18 @@ class ShowSeq {
42024
42024
  for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
42025
42025
  if(strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
42026
42026
  if(i != il - 1) { // modify
42027
- strandArray[i + 1].loopResCnt += strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
42027
+ strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + strandArray[i].endRefnum - strandArray[i].startRefnum + 1;
42028
42028
  }
42029
42029
 
42030
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  strandArray.splice(i, 1);
42031
42031
  }
42032
42032
  }
42033
-
42033
+
42034
42034
  // 3. assign refnumLabel for each resid
42035
42035
  strandCnt = 0;
42036
42036
  let loopCnt = 0;
42037
42037
 
42038
- let bNterminal = true, bCterminal = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
42038
+ let bBeforeAstrand = true, bAfterGstrand = true, refnumLabelNoPostfix, prevStrandCnt = 0, currRefnum;
42039
42039
  bStart = false;
42040
42040
  let refnumInStrand = 0;
42041
42041
  if(strandArray.length > 0) {
@@ -42054,7 +42054,7 @@ class ShowSeq {
42054
42054
  let firstChar = refnumLabel.substr(0,1);
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42055
  if(!bStart && (firstChar == ' ' || firstChar == 'A' || firstChar == 'B')) { // start of a new IG domain
42056
42056
  bStart = true;
42057
- bNterminal = true;
42057
+ bBeforeAstrand = true;
42058
42058
  loopCnt = 0;
42059
42059
  }
42060
42060
  }
@@ -42069,29 +42069,48 @@ class ShowSeq {
42069
42069
  if(parseInt(currResi) < parseInt(strandArray[strandCnt].startResi)) {
42070
42070
  ic.residIgLoop[residueid] = 1;
42071
42071
 
42072
- if(bNterminal) { // make it continuous to the 1st strand
42072
+ if(bBeforeAstrand) { // make it continuous to the 1st strand
42073
42073
  if(bStart) {
42074
42074
  currRefnum = strandArray[strandCnt].startRefnum - strandArray[strandCnt].loopResCnt + loopCnt;
42075
42075
  refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
42076
42076
  refnumLabel = refnumLabelNoPostfix + strandArray[strandCnt].strandPostfix;
42077
- }
42077
+ }
42078
+ else {
42079
+ //loopCnt = 0;
42080
+ refnumLabelNoPostfix = undefined;
42081
+ refnumLabel = undefined;
42082
+ }
42078
42083
  }
42079
42084
  else {
42080
- //currStrand = strandArray[prevStrandCnt].strand;
42081
-
42082
42085
  if(prevStrandCnt >= 0 && strandArray[prevStrandCnt].strand.substr(0, 1) == 'G') {
42083
- if(bStart && ic.resid2refnum[residueid]) {
42084
- currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42085
- refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42086
- refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42086
+ if(!bAfterGstrand) {
42087
+ //loopCnt = 0;
42088
+ refnumLabelNoPostfix = undefined;
42089
+ refnumLabel = undefined;
42087
42090
  }
42088
42091
  else {
42089
- bStart = false;
42090
- bNterminal = true;
42091
- loopCnt = 0;
42092
+ if(bStart && ic.resid2refnum[residueid]) {
42093
+ bAfterGstrand = true;
42094
+
42095
+ currRefnum = strandArray[prevStrandCnt].endRefnum + loopCnt;
42096
+ refnumLabelNoPostfix = strandArray[prevStrandCnt].strand + currRefnum;
42097
+ refnumLabel = refnumLabelNoPostfix + strandArray[prevStrandCnt].strandPostfix;
42098
+ }
42099
+ else {
42100
+ bStart = false;
42101
+ bBeforeAstrand = true;
42102
+ //loopCnt = 0;
42103
+
42104
+ bAfterGstrand = false;
42105
+
42106
+ refnumLabelNoPostfix = undefined;
42107
+ refnumLabel = undefined;
42108
+ }
42092
42109
  }
42093
42110
  }
42094
42111
  else {
42112
+ bAfterGstrand = true; // reset
42113
+
42095
42114
  let len = strandArray[strandCnt].loopResCnt;
42096
42115
  let halfLen = parseInt(len / 2.0 + 0.5);
42097
42116
 
@@ -42109,8 +42128,7 @@ class ShowSeq {
42109
42128
  }
42110
42129
  }
42111
42130
  else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
42112
- bNterminal = false;
42113
- //bCterminal = true; // The next will be C-terminal
42131
+ bBeforeAstrand = false;
42114
42132
 
42115
42133
  if(strandArray[strandCnt].anchorRefnum) { // use anchor to name refnum
42116
42134
  if(currResi == strandArray[strandCnt].startResi) {
@@ -42137,23 +42155,20 @@ class ShowSeq {
42137
42155
  else if(parseInt(currResi) > parseInt(strandArray[strandCnt].endResi)) {
42138
42156
  ic.residIgLoop[residueid] = 1;
42139
42157
 
42140
- if(!bCterminal) {
42158
+ if(!bAfterGstrand) {
42141
42159
  refnumLabelNoPostfix = undefined;
42142
42160
  refnumLabel = undefined;
42143
42161
  }
42144
42162
  else {
42145
42163
  // C-terminal
42146
42164
  if(!ic.resid2refnum[residueid]) {
42147
- //break;
42148
-
42149
- bCterminal = false;
42150
- //bNterminal = true; // The next will be N-terminal
42165
+ bAfterGstrand = false;
42151
42166
 
42152
42167
  refnumLabelNoPostfix = undefined;
42153
42168
  refnumLabel = undefined;
42154
42169
  }
42155
42170
  else {
42156
- bCterminal = true;
42171
+ bAfterGstrand = true;
42157
42172
 
42158
42173
  currRefnum = strandArray[strandCnt].endRefnum + loopCnt;
42159
42174
  refnumLabelNoPostfix = strandArray[strandCnt].strand + currRefnum;
@@ -42289,7 +42304,8 @@ class ShowSeq {
42289
42304
  let color = this.getRefnumColor(currStrand, true);
42290
42305
  let colorStr = (!bLoop) ? 'style="color:' + color + '; text-decoration: underline overline;"' : 'style="color:' + color + '"';
42291
42306
 
42292
- let lastTwo = parseInt(refnum.substr(refnum.length - 2, 2));
42307
+ let lastTwoStr = refnum.substr(refnum.length - 2, 2);
42308
+ let lastTwo = parseInt(lastTwoStr);
42293
42309
  parseInt(refnum.substr(refnum.length - 3, 3));
42294
42310
 
42295
42311
  let html = '';
@@ -42302,7 +42318,7 @@ class ShowSeq {
42302
42318
  }
42303
42319
  else if(refnumLabel && lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
42304
42320
  // e.g., 2152a
42305
- let lastTwoStr = isNaN(refnumStr) ? lastTwo + refnumStr.substr(refnumStr.length - 1, 1) : lastTwo;
42321
+ lastTwoStr = isNaN(refnumStr) ? lastTwoStr + refnumStr.substr(refnumStr.length - 1, 1) : lastTwoStr;
42306
42322
  html += '<span ' + colorStr + ' title="' + refnumLabel + '">' + lastTwoStr + '</span>';
42307
42323
  }
42308
42324
  else {