From: tcofoegbu Date: Mon, 1 May 2017 17:13:55 +0000 (+0100) Subject: JAL-2482 bug fix X-Git-Tag: Release_2_10_2~3^2~116 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=95b34183f11c22462b60bc5c0254d66eba1c1f19;p=jalview.git JAL-2482 bug fix --- diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index c69581f..fe3a25b 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -575,18 +575,8 @@ public class SiftsClient implements SiftsClientI .equalsIgnoreCase(seqCoordSys.getName()) && isAccessionMatched(cRefDb.getDbAccessionId())) { - String resNumIndexString = cRefDb.getDbResNum() - .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED) - : cRefDb.getDbResNum(); - try - { - currSeqIndex = Integer.valueOf(resNumIndexString); - } catch (NumberFormatException nfe) - { - currSeqIndex = Integer.valueOf(resNumIndexString - .split("[a-zA-Z]")[0]); - continue; - } + currSeqIndex = getLeadingIntegerValue( + cRefDb.getDbResNum(), UNASSIGNED); if (pdbRefDb != null) { break;// exit loop if pdb and uniprot are already found @@ -599,23 +589,11 @@ public class SiftsClient implements SiftsClientI } if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd()) { - int resNum; - try - { - resNum = (pdbRefDb == null) ? Integer.valueOf(residue - .getDbResNum()) : Integer.valueOf(pdbRefDb - .getDbResNum()); - } catch (NumberFormatException nfe) - { - if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null")) - { - resNum = UNASSIGNED; - continue; - } - resNum = Integer.valueOf(pdbRefDb - .getDbResNum().split("[a-zA-Z]")[0]); - continue; - } + + int resNum = (pdbRefDb == null) ? getLeadingIntegerValue( + residue.getDbResNum(), UNASSIGNED) + : getLeadingIntegerValue(pdbRefDb.getDbResNum(), + UNASSIGNED); if (isResidueObserved(residue) || seqCoordSys == CoordinateSys.UNIPROT) @@ -638,6 +616,30 @@ public class SiftsClient implements SiftsClientI } /** + * Get the leading integer part of a string that begins with an integer. + * + * @param input + * - the string input to process + * @param failValue + * - value returned if unsuccessful + * @return + */ + static int getLeadingIntegerValue(String input, int failValue) + { + if (input == null) + { + return failValue; + } + String[] parts = input.split("(?=\\D)(?<=\\d)"); + if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+")) + { + return Integer.valueOf(parts[0]); + } + return failValue; + } + + + /** * * @param chainId * Target chain to populate mapping of its atom positions.