X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;fp=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=26291ebf182f75b5526280d545e880db0f85e0f4;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=b0bea88c21171b42b8c30d81add4b5dadac56b12;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java index b0bea88..26291eb 100644 --- a/src/jalview/ws/dbsources/Xfam.java +++ b/src/jalview/ws/dbsources/Xfam.java @@ -57,27 +57,26 @@ public abstract class Xfam extends DbSourceProxyImpl // retrieved. startQuery(); // TODO: trap HTTP 404 exceptions and return null - String xfamUrl = getXFAMURL() - + queries.trim().toUpperCase() + getXFAMURLSUFFIX(); + String xfamUrl = getXFAMURL() + queries.trim().toUpperCase() + + getXFAMURLSUFFIX(); if (Cache.log != null) { Cache.log.debug("XFAM URL for retrieval is: " + xfamUrl); } - AlignmentI rcds = new FormatAdapter().readFile(xfamUrl , + AlignmentI rcds = new FormatAdapter().readFile(xfamUrl, DataSourceType.URL, FileFormat.Stockholm); for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++) { rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(), - // getDbSource(), + // getDbSource(), getDbVersion(), queries.trim().toUpperCase())); if (!getDbSource().equals(getXfamSource())) { // add the specific ref too - rcds.getSequenceAt(s).addDBRef( - new DBRefEntry(getDbSource(), getDbVersion(), queries - .trim().toUpperCase())); + rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), + getDbVersion(), queries.trim().toUpperCase())); } } stopQuery();