From 006363dc999cef4e9c49dd6a38ea0d78cbb62472 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Fri, 10 Jan 2014 16:35:28 +0000 Subject: [PATCH] Apply formatting --- datadb/compbio/beans/DateBean.java | 11 ++-- datadb/compbio/beans/JobBean.java | 41 ++++++++------- datadb/compbio/beans/ProteinBean.java | 55 ++++++++++---------- datadb/compbio/beans/Total.java | 22 ++++---- datadb/compbio/beans/TotalByCounterBean.java | 8 +-- datadb/compbio/beans/TotalJobsStatisticBean.java | 13 ++--- datadb/compbio/beans/UserBean.java | 28 +++++----- .../cassandra/CassandraNativeConnector.java | 22 ++++---- datadb/compbio/cassandra/CassandraReaderOld.java | 7 +-- datadb/compbio/cassandra/CassandraRemover.java | 43 ++++++++------- datadb/compbio/cassandra/CassandraUserManager.java | 10 ++-- datadb/compbio/cassandra/CassandraWriter.java | 1 - datadb/compbio/cassandra/DataBase.java | 32 ++++++------ datadb/compbio/cassandra/DateFormatter.java | 13 +++-- datadb/compbio/cassandra/JpredParser.java | 8 +-- datadb/compbio/cassandra/JpredParserHTTP.java | 1 + datadb/compbio/cassandra/JpredParserLocalFile.java | 4 +- datadb/compbio/cassandra/PredictionIndex.java | 4 +- .../compbio/cassandra/readers/CassandraReader.java | 7 ++- .../readers/CassandraReaderExecutionTime.java | 8 --- .../cassandra/readers/DailyStatisticsReader.java | 25 ++++----- datadb/compbio/cassandra/readers/IpReader.java | 6 +-- datadb/compbio/cassandra/readers/JobReader.java | 2 +- .../cassandra/readers/PredictionReader.java | 22 ++++---- datadb/compbio/cassandra/readers/ProteoDAO.java | 5 +- .../compbio/cassandra/readers/ReaderByCounter.java | 29 +++++------ .../compbio/cassandra/readers/SequenceReader.java | 21 ++++---- engine/compbio/engine/Job.java | 28 +++++----- engine/compbio/engine/JpredJob.java | 4 +- .../engine/ProteoCachePropertyHelperManager.java | 44 +++++++--------- engine/compbio/engine/archive/Archive.java | 15 +++--- engine/compbio/engine/archive/ArchiveManager.java | 53 ++++++++----------- engine/compbio/engine/archive/ArchivedJob.java | 2 +- 33 files changed, 282 insertions(+), 312 deletions(-) diff --git a/datadb/compbio/beans/DateBean.java b/datadb/compbio/beans/DateBean.java index bddd7de..7c593d3 100644 --- a/datadb/compbio/beans/DateBean.java +++ b/datadb/compbio/beans/DateBean.java @@ -6,28 +6,27 @@ import java.util.Map; public class DateBean { private String date; - private Map jobidAndSeq; // Map for jobid and sequence - + private Map jobidAndSeq; // Map for jobid and sequence + public DateBean() { this.jobidAndSeq = new HashMap(); } - + public DateBean(String date) { this.date = date; this.jobidAndSeq = new HashMap(); } - + public void setJobidAndSeq(String jobid, String seq) { if (jobidAndSeq == null) jobidAndSeq = new HashMap(); jobidAndSeq.put(jobid, seq); } - public Map getJobidAndSeq() { return jobidAndSeq; } - + public void setDate(String date) { this.date = date; } diff --git a/datadb/compbio/beans/JobBean.java b/datadb/compbio/beans/JobBean.java index 0a15062..8176748 100644 --- a/datadb/compbio/beans/JobBean.java +++ b/datadb/compbio/beans/JobBean.java @@ -10,47 +10,48 @@ public class JobBean implements PredictionIndex { private String dateStart; private String dateEnd; private String sequence; - private String ip; - private LinkedHashMap predictions; - - public JobBean (String seq, String id, String dateStart, String dateEnd, String ip, Map pred) { + private String ip; + private LinkedHashMap predictions; + + public JobBean(String seq, String id, String dateStart, String dateEnd, String ip, Map pred) { this.sequence = seq; this.jobid = id; this.dateStart = dateStart; this.dateEnd = dateEnd; this.ip = ip; - this.predictions = new LinkedHashMap(); + this.predictions = new LinkedHashMap(); setPredictions(pred); } - - public void setPredictions(Map pred) { + + public void setPredictions(Map pred) { if (predictions == null) - predictions = new LinkedHashMap(); + predictions = new LinkedHashMap(); for (String index : predIndex) { this.predictions.put(index, pred.get(index)); - } + } } - public String getSequence () { + + public String getSequence() { return sequence; } - - public String getJobid () { + + public String getJobid() { return jobid; } - - public String getDateStart () { + + public String getDateStart() { return dateStart; } - - public String getDateEnd () { + + public String getDateEnd() { return dateEnd; } - - public String getIp () { + + public String getIp() { return ip; } - - public Map getPrediction () { + + public Map getPrediction() { return predictions; } } diff --git a/datadb/compbio/beans/ProteinBean.java b/datadb/compbio/beans/ProteinBean.java index b1e2c2f..c649320 100644 --- a/datadb/compbio/beans/ProteinBean.java +++ b/datadb/compbio/beans/ProteinBean.java @@ -7,65 +7,66 @@ import java.util.Map; import compbio.cassandra.PredictionIndex; -public class ProteinBean implements PredictionIndex{ +public class ProteinBean implements PredictionIndex { private String sequence; private String jnetpred; private List jobid; - private LinkedHashMap predictions; - private List subProt; // protein sequence divided by several parts for highlighting the particular part + private LinkedHashMap predictions; + private List subProt; // protein sequence divided by several parts + // for highlighting the particular part private int size; - - public ProteinBean (String seq, Map pred) { + + public ProteinBean(String seq, Map pred) { this.sequence = seq; - this.predictions = new LinkedHashMap(); + this.predictions = new LinkedHashMap(); this.jobid = new ArrayList(); setPredictions(pred); } - - public void setSequence (String seq) { + + public void setSequence(String seq) { this.sequence = seq; } - - public void setPredictions(Map pred) { + + public void setPredictions(Map pred) { if (predictions == null) - predictions = new LinkedHashMap(); + predictions = new LinkedHashMap(); for (String index : predIndex) { this.predictions.put(index, pred.get(index)); - } + } this.size = predictions.size(); } - - public String getSequence () { + + public String getSequence() { return sequence; } - - public String getJnetpred () { + + public String getJnetpred() { return jnetpred; } - - public void setJnetpred (Map pred) { + + public void setJnetpred(Map pred) { if (pred != null) { - if (pred.containsKey("jnetpred")) + if (pred.containsKey("jnetpred")) jnetpred = pred.get("jnetpred"); } } - - public List getJobid () { + + public List getJobid() { return jobid; } - - public void setJobid (String id) { + + public void setJobid(String id) { this.jobid.add(id); } - public int getSize () { + public int getSize() { return size; } - - public LinkedHashMap getPredictions () { + + public LinkedHashMap getPredictions() { return predictions; } - + public void setSubProt(List subProt) { this.subProt = subProt; } diff --git a/datadb/compbio/beans/Total.java b/datadb/compbio/beans/Total.java index 3e819ed..64813ee 100644 --- a/datadb/compbio/beans/Total.java +++ b/datadb/compbio/beans/Total.java @@ -6,21 +6,21 @@ package compbio.beans; * @param total * total number of jobs for a day * @param totalOK - * number of jobs with execution status OK for a date + * number of jobs with execution status OK for a date * @param totalStopped - * number of jobs with execution status STOPPED for a date + * number of jobs with execution status STOPPED for a date * @param totalError - * number of jobs with execution status Jpred ERROR for a date + * number of jobs with execution status Jpred ERROR for a date * @param totalTimeOut - * number of jobs with execution status TIMEDOUT for a date + * number of jobs with execution status TIMEDOUT for a date */ public class Total { - private long total; - private long totalOK; - private long totalStopped; - private long totalError; - private long totalTimeOut; - + private long total; + private long totalOK; + private long totalStopped; + private long totalError; + private long totalTimeOut; + public Total(long total, long totalOK, long totalStopped, long totalError, long totalTimeOut) { this.total = total; this.totalOK = totalOK; @@ -28,7 +28,7 @@ public class Total { this.totalError = totalError; this.totalTimeOut = totalTimeOut; } - + public void setTotal(long tot) { this.total = tot; } diff --git a/datadb/compbio/beans/TotalByCounterBean.java b/datadb/compbio/beans/TotalByCounterBean.java index bfe3b23..5ab3d89 100644 --- a/datadb/compbio/beans/TotalByCounterBean.java +++ b/datadb/compbio/beans/TotalByCounterBean.java @@ -1,9 +1,9 @@ package compbio.beans; public class TotalByCounterBean { - private int totaljobs; // total jobs for current condition - private String name; // name for counter condition (ip or sequence) - + private int totaljobs; // total jobs for current condition + private String name; // name for counter condition (ip or sequence) + public void setTotaljobs(int tot) { this.totaljobs = tot; } @@ -11,7 +11,7 @@ public class TotalByCounterBean { public int getTotaljobs() { return totaljobs; } - + public void setName(String name) { this.name = name; } diff --git a/datadb/compbio/beans/TotalJobsStatisticBean.java b/datadb/compbio/beans/TotalJobsStatisticBean.java index 1c74a27..5653f7a 100644 --- a/datadb/compbio/beans/TotalJobsStatisticBean.java +++ b/datadb/compbio/beans/TotalJobsStatisticBean.java @@ -7,18 +7,19 @@ import java.util.Map; * bean for a report of daily statistics. * * @param dateTotal - * Map where String - a date, Total - total info for jobs with different status + * Map where String - a date, Total - total info for + * jobs with different status * @param wholeTotal - * total sum for each parameter from dateTotal + * total sum for each parameter from dateTotal */ public class TotalJobsStatisticBean { private Map dateTotal; private Total wholeTotal; - + public TotalJobsStatisticBean() { this.dateTotal = new LinkedHashMap(); } - + public void setDateTotal(String dat, Total tot) { if (this.dateTotal == null) dateTotal = new LinkedHashMap(); @@ -28,11 +29,11 @@ public class TotalJobsStatisticBean { public Map getDateTotal() { return dateTotal; } - + public void setWholeTotal(Total tot) { this.wholeTotal = tot; } - + public Total getWholeTotal() { return wholeTotal; } diff --git a/datadb/compbio/beans/UserBean.java b/datadb/compbio/beans/UserBean.java index 77c6724..a0f396a 100644 --- a/datadb/compbio/beans/UserBean.java +++ b/datadb/compbio/beans/UserBean.java @@ -1,37 +1,35 @@ package compbio.beans; -import java.util.ArrayList; -import java.util.Arrays; + import java.util.HashMap; -import java.util.List; import java.util.Map; - public class UserBean { private String ip; - private Map mainInfo; // store jobid, date start and sequence - + private Map mainInfo; // store jobid, date start and + // sequence + public UserBean(String ip) { this.ip = ip; - mainInfo = new HashMap(); + mainInfo = new HashMap(); } public String getIp() { return ip; } - + public void setMainInfo(String jobid, String date, String sequence) { if (mainInfo == null) - mainInfo = new HashMap(); - mainInfo.put(jobid, new String[] {date, sequence}); + mainInfo = new HashMap(); + mainInfo.put(jobid, new String[] { date, sequence }); } - - public void setMainInfo( Map info) { + + public void setMainInfo(Map info) { if (mainInfo == null) - mainInfo = new HashMap(); + mainInfo = new HashMap(); mainInfo = info; } - - public Map getMainInfo() { + + public Map getMainInfo() { return mainInfo; } diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java index 5e5cf5a..9d8d01d 100644 --- a/datadb/compbio/cassandra/CassandraNativeConnector.java +++ b/datadb/compbio/cassandra/CassandraNativeConnector.java @@ -33,7 +33,7 @@ public class CassandraNativeConnector { public static String CASSANDRA_HOSTNAME = "localhost"; - public static Session getSession () { + public static Session getSession() { return session; } @@ -49,7 +49,7 @@ public class CassandraNativeConnector { Cluster.Builder builder = Cluster.builder(); builder.addContactPoint(CASSANDRA_HOSTNAME); - //PrintClusterConfiguration( builder.getConfiguration()); + // PrintClusterConfiguration( builder.getConfiguration()); cluster = builder.build(); Metadata metadata = cluster.getMetadata(); @@ -66,9 +66,8 @@ public class CassandraNativeConnector { session.execute("CREATE KEYSPACE IF NOT EXISTS ProteinKeyspace WITH replication = {'class':'SimpleStrategy', 'replication_factor':3};"); session.execute("USE ProteinKeyspace"); - session.execute("CREATE TABLE IF NOT EXISTS MainParameters " - + "(Name ascii, Value ascii, PRIMARY KEY(Name));"); - + session.execute("CREATE TABLE IF NOT EXISTS MainParameters " + "(Name ascii, Value ascii, PRIMARY KEY(Name));"); + session.execute("CREATE TABLE IF NOT EXISTS ProteinRow " + "(Protein ascii, JobID ascii, Predictions map, PRIMARY KEY(JobID));"); @@ -81,7 +80,7 @@ public class CassandraNativeConnector { session.execute("CREATE TABLE IF NOT EXISTS FailLog " + "(jobtime bigint, JobID ascii, ExecTime int, ip ascii, FinalStatus ascii, PRIMARY KEY(jobtime, JobID));"); - + session.execute("CREATE TABLE IF NOT EXISTS JpredArchive " + "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, FinalStatus ascii, ExecutionStatus ascii, alignment map, " + "predictions map, ArchiveLink varchar, LOG varchar, PRIMARY KEY(JobID));"); @@ -91,8 +90,7 @@ public class CassandraNativeConnector { String com = "CREATE TABLE IF NOT EXISTS Users " + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));"; - - + try { session.execute(com); } catch (QueryExecutionException e) { @@ -112,8 +110,8 @@ public class CassandraNativeConnector { session.execute("CREATE INDEX IF NOT EXISTS ON ProteinLog (ExecutionStatus);"); session.execute("CREATE INDEX IF NOT EXISTS ON FailLog (FinalStatus);"); session.execute("CREATE INDEX IF NOT EXISTS ON Users (email);"); - // session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);"); - } + // session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);"); + } public void Closing() { session.shutdown(); @@ -136,14 +134,14 @@ public class CassandraNativeConnector { Calendar cal = Calendar.getInstance(); return cal.getTimeInMillis(); } - + private void PrintClusterConfiguration(Configuration cc) { Policies policies = cc.getPolicies(); SocketOptions sopt = cc.getSocketOptions(); ProtocolOptions propt = cc.getProtocolOptions(); PoolingOptions plopt = cc.getPoolingOptions(); MetricsOptions mopt = cc.getMetricsOptions(); - QueryOptions qopt = cc.getQueryOptions(); + QueryOptions qopt = cc.getQueryOptions(); System.out.println("Cluster configuration:"); System.out.println(" Policies = " + policies.toString()); System.out.println(" Socket Options = " + sopt.toString()); diff --git a/datadb/compbio/cassandra/CassandraReaderOld.java b/datadb/compbio/cassandra/CassandraReaderOld.java index 852beb0..c7176b0 100644 --- a/datadb/compbio/cassandra/CassandraReaderOld.java +++ b/datadb/compbio/cassandra/CassandraReaderOld.java @@ -221,7 +221,7 @@ public class CassandraReaderOld { for (Row r : rows) { String prot = r.getString("Protein"); String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class)); - if (prot != null || prediction != null) + if (prot != null || prediction != null) res.put(prot, prediction); } final long endTime = System.currentTimeMillis(); @@ -229,13 +229,14 @@ public class CassandraReaderOld { return res; } - private String findJnetpred (Map pred) { + private String findJnetpred(Map pred) { if (pred != null) { - if (pred.containsKey("jnetpred")) + if (pred.containsKey("jnetpred")) return pred.get("jnetpred"); } return null; } + /* * getting protein sequences by counter */ diff --git a/datadb/compbio/cassandra/CassandraRemover.java b/datadb/compbio/cassandra/CassandraRemover.java index d7ebd87..48a5893 100644 --- a/datadb/compbio/cassandra/CassandraRemover.java +++ b/datadb/compbio/cassandra/CassandraRemover.java @@ -14,19 +14,19 @@ import com.datastax.driver.core.Session; public class CassandraRemover { private Session session; - static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd"); + static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd"); private static Logger log = Logger.getLogger(CassandraNativeConnector.class); public CassandraRemover() { Session inis = CassandraNativeConnector.getSession(); - setSession (inis); + setSession(inis); } public void setSession(Session s) { assert s != null; session = s; } - + /* * delete a record from CF for current jobId */ @@ -42,7 +42,7 @@ public class CassandraRemover { System.out.println("Command: " + com); ResultSet results = session.execute(com); Row row = results.one(); - long njobs = row.getLong("Total") -1 ; + long njobs = row.getLong("Total") - 1; if (status.equals("OK")) { long njobsOK = row.getLong("TotalOK") - 1; String com1 = "DELETE FROM ProteinRow WHERE JobID = '" + jobid + "';"; @@ -69,24 +69,24 @@ public class CassandraRemover { } System.out.println("Remove jobs: " + jobid); } - + private void UpdateJobDateInfo(long date, String ColumnName, long totalcol, long total) { String com4 = "UPDATE JobDateInfo SET " + ColumnName + " = " + totalcol + ", Total = " + total + " WHERE jobday = " + date + ";"; System.out.println("Command: " + com4); session.execute(com4); } - - public int RemoveJobById (String jobid) { - if (jobid == null) + + public int RemoveJobById(String jobid) { + if (jobid == null) return 0; Long date = FindDate(jobid); RemoveJob(jobid, date); return 1; } - - public int RemoveJobByDate (String date1, String date2) { + + public int RemoveJobByDate(String date1, String date2) { int numremover = 0; - if (date1 == null || date2 == null) + if (date1 == null || date2 == null) return 0; Long dateBegin = convertDate(date1); Long dateEnd = convertDate(date2); @@ -127,11 +127,10 @@ public class CassandraRemover { } return numremover; } - - - public int RemoveJobByIp (String ip) { + + public int RemoveJobByIp(String ip) { int numremover = 0; - if (ip == null) + if (ip == null) return 0; String com = "SELECT databegin, JobID FROM ProteinLog WHERE ip = '" + ip + "';"; ResultSet results = session.execute(com); @@ -148,10 +147,10 @@ public class CassandraRemover { } return numremover; } - - public int RemoveJobBySequence (String seq) { + + public int RemoveJobBySequence(String seq) { int numremover = 0; - if (seq == null) + if (seq == null) return 0; String com = "SELECT JobID FROM ProteinRow WHERE Protein = '" + seq + "';"; ResultSet results = session.execute(com); @@ -166,14 +165,14 @@ public class CassandraRemover { } return numremover; } - + private Long FindDate(String jobid) { String com = "SELECT databegin FROM ProteinLog WHERE JobID = '" + jobid + "';"; ResultSet results = session.execute(com); Long date = convertDate(results.one().getString("databegin")); return date; } - + private String FindStatus(String jobid) { String com = "SELECT FinalStatus FROM ProteinLog WHERE JobID = '" + jobid + "';"; System.out.println("Command: " + com); @@ -182,8 +181,8 @@ public class CassandraRemover { System.out.println("*****status: " + status); return status; } - - protected long convertDate (String d) { + + protected long convertDate(String d) { try { if (null != d) { Date startdate = dateformatter.parse(d); diff --git a/datadb/compbio/cassandra/CassandraUserManager.java b/datadb/compbio/cassandra/CassandraUserManager.java index e2158f7..f810107 100644 --- a/datadb/compbio/cassandra/CassandraUserManager.java +++ b/datadb/compbio/cassandra/CassandraUserManager.java @@ -37,7 +37,7 @@ public class CassandraUserManager implements UserManager { if (0 < users.all().size()) { throw new DataIntegrityViolationException("A user with email " + user.getEmail() + " exists"); } - + } catch (QueryExecutionException e) { String mess = "CassandraUserManagerImpl.addUser: query execution exception..."; System.out.println(mess); @@ -62,7 +62,8 @@ public class CassandraUserManager implements UserManager { String test = list.get(0).getString("Value"); id = Long.parseLong(test, 10); } else { - // if the MaxUserId parameter does not exist it is inserted with id = 1 + // if the MaxUserId parameter does not exist it is inserted + // with id = 1 id = 0; } id++; @@ -84,9 +85,8 @@ public class CassandraUserManager implements UserManager { } String incom = "INSERT INTO Users (name, id, email, password, organisation, position, signedtolist, registrationdate) VALUES ('" - + user.getFullName() + "'," + id + ",'" + user.getEmail() + "','" + user.getPassword() + "','" - + user.getOrganisation() + "','" + user.getPosition() + "'," + user.isUpdateByEmail() + "," - + user.getRegistrationDate().getTime() + ");"; + + user.getFullName() + "'," + id + ",'" + user.getEmail() + "','" + user.getPassword() + "','" + user.getOrganisation() + + "','" + user.getPosition() + "'," + user.isUpdateByEmail() + "," + user.getRegistrationDate().getTime() + ");"; try { session.execute(incom); } catch (QueryExecutionException e) { diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java index f20f457..710d78b 100644 --- a/datadb/compbio/cassandra/CassandraWriter.java +++ b/datadb/compbio/cassandra/CassandraWriter.java @@ -3,7 +3,6 @@ package compbio.cassandra; import java.util.List; import org.apache.log4j.Logger; -import org.springframework.dao.DataIntegrityViolationException; import com.datastax.driver.core.Row; import com.datastax.driver.core.Session; diff --git a/datadb/compbio/cassandra/DataBase.java b/datadb/compbio/cassandra/DataBase.java index 7c3cc82..e741b39 100644 --- a/datadb/compbio/cassandra/DataBase.java +++ b/datadb/compbio/cassandra/DataBase.java @@ -9,16 +9,16 @@ import compbio.beans.ProteinBean; public class DataBase { private String date; - private int total; // total number of jobs - private int totalOK; // number of jobs with execution status OK - private int totalStopped; // number of jobs with execution status STOPPED - private int totalError; // number of jobs with execution status Jpred ERROR - private int totalTimeOut; // number of jobs with execution status TIMEOUT + private int total; // total number of jobs + private int totalOK; // number of jobs with execution status OK + private int totalStopped; // number of jobs with execution status STOPPED + private int totalError; // number of jobs with execution status Jpred ERROR + private int totalTimeOut; // number of jobs with execution status TIMEOUT private int totalJobs; - private int totalId; // total jobs for current protein sequence + private int totalId; // total jobs for current protein sequence private String id; private String ip; - private String prot; // protein sequence + private String prot; // protein sequence private String jpred; private List timeRez; private List timeTotalExec; @@ -82,7 +82,7 @@ public class DataBase { public int getTotalTimeOut() { return totalTimeOut; } - + public void setTotalJobs(int totalJobs) { this.totalJobs = totalJobs; } @@ -122,7 +122,7 @@ public class DataBase { public String getId() { return id; } - + public void setIp(String ip) { this.ip = ip; } @@ -138,7 +138,7 @@ public class DataBase { public List getTimeRez() { return timeRez; } - + public void setTimeTotalExec(List timeTotalExec) { this.timeTotalExec = timeTotalExec; } @@ -146,19 +146,19 @@ public class DataBase { public List getTimeTotalExec() { return timeTotalExec; } - - public void setLogInfo(JobBean logInfo){ + + public void setLogInfo(JobBean logInfo) { this.logInfo = logInfo; } - + public JobBean getLogInfo() { return logInfo; } - - public void setPredictions(ProteinBean predictions){ + + public void setPredictions(ProteinBean predictions) { this.predictions = predictions; } - + public ProteinBean getPredictions() { return predictions; } diff --git a/datadb/compbio/cassandra/DateFormatter.java b/datadb/compbio/cassandra/DateFormatter.java index 471f2a8..2fa7708 100644 --- a/datadb/compbio/cassandra/DateFormatter.java +++ b/datadb/compbio/cassandra/DateFormatter.java @@ -7,7 +7,7 @@ import java.util.Date; public class DateFormatter { private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd"); private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy"); - + /* * convert String date into long date (miliseconds since the epoch start) */ @@ -24,10 +24,9 @@ public class DateFormatter { } return dateWorkSt; } - + /* - * date validator - * true - if valid date, false - if invalid + * date validator true - if valid date, false - if invalid */ public static boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) { if (dateToValidate == null || dateToValidate.equals("")) { @@ -43,7 +42,7 @@ public class DateFormatter { } return true; } - + /* * convert date from long to String */ @@ -51,11 +50,11 @@ public class DateFormatter { String dateString = formatter.format(new Date(indate)); return dateString; } - + public static SimpleDateFormat getFormatYYMMDD() { return formatYYMMDD; } - + public static SimpleDateFormat getFormatDDMMYY() { return formatDDMMYY; } diff --git a/datadb/compbio/cassandra/JpredParser.java b/datadb/compbio/cassandra/JpredParser.java index 27020ec..ae7abab 100644 --- a/datadb/compbio/cassandra/JpredParser.java +++ b/datadb/compbio/cassandra/JpredParser.java @@ -6,11 +6,11 @@ public interface JpredParser { /* * Defines a source file with metainformation of Jpred Jobs - **/ - void setSource (String newsourceprefix); - + */ + void setSource(String newsourceprefix); + /* * Makes real parsing of the source file - **/ + */ void Parsing(String source, int nDays) throws IOException; } diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java index 453f01f..d221209 100644 --- a/datadb/compbio/cassandra/JpredParserHTTP.java +++ b/datadb/compbio/cassandra/JpredParserHTTP.java @@ -93,6 +93,7 @@ public class JpredParserHTTP implements JpredParser { } return protein; } + private String parseSeqFile(final InputStream stream, String jobid) throws FileNotFoundException { final FastaReader fr = new FastaReader(stream); String protein = ""; diff --git a/datadb/compbio/cassandra/JpredParserLocalFile.java b/datadb/compbio/cassandra/JpredParserLocalFile.java index f48178c..e2e5dc9 100644 --- a/datadb/compbio/cassandra/JpredParserLocalFile.java +++ b/datadb/compbio/cassandra/JpredParserLocalFile.java @@ -106,7 +106,9 @@ public class JpredParserLocalFile implements JpredParser { } catch (ParseException e) { e.printStackTrace(); } - //countinsertions += cw.FormQueryTables(insertdate, starttime, finishtime, ip, id, "OK", "OK", newprotein, seqs); + // countinsertions += cw.FormQueryTables(insertdate, + // starttime, finishtime, ip, id, "OK", "OK", + // newprotein, seqs); } fr.close(); } catch (IOException e) { diff --git a/datadb/compbio/cassandra/PredictionIndex.java b/datadb/compbio/cassandra/PredictionIndex.java index d184650..9966668 100644 --- a/datadb/compbio/cassandra/PredictionIndex.java +++ b/datadb/compbio/cassandra/PredictionIndex.java @@ -5,6 +5,6 @@ public interface PredictionIndex { /** * Ordering indexes for predictions */ - public final String[] predIndex = {"jnetpred", "JNETCONF", "JNETHMM", "JNETPSSM", "JNETSOL0", "JNETSOL5", - "JNETSOL25", "Lupas_14", "Lupas_21", "Lupas_28"}; + public final String[] predIndex = { "jnetpred", "JNETCONF", "JNETHMM", "JNETPSSM", "JNETSOL0", "JNETSOL5", "JNETSOL25", "Lupas_14", + "Lupas_21", "Lupas_28" }; } diff --git a/datadb/compbio/cassandra/readers/CassandraReader.java b/datadb/compbio/cassandra/readers/CassandraReader.java index 50db7a0..7de48e6 100644 --- a/datadb/compbio/cassandra/readers/CassandraReader.java +++ b/datadb/compbio/cassandra/readers/CassandraReader.java @@ -22,7 +22,7 @@ public class CassandraReader { assert s != null; session = s; } - + protected ResultSet CassandraQuery(String command) { try { ResultSet results = session.execute(command); @@ -40,9 +40,9 @@ public class CassandraReader { log.error(e.getLocalizedMessage(), e.getCause()); return null; } - + } - + /* * find the earliest date in the database */ @@ -51,5 +51,4 @@ public class CassandraReader { return earlestDate; } - } diff --git a/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java index 3e8453e..134a139 100644 --- a/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java +++ b/datadb/compbio/cassandra/readers/CassandraReaderExecutionTime.java @@ -1,22 +1,14 @@ package compbio.cassandra.readers; - import java.util.Calendar; import java.util.List; import java.util.ArrayList; -import org.apache.log4j.Logger; - import com.datastax.driver.core.Row; import com.datastax.driver.core.Session; import com.datastax.driver.core.ResultSet; -import com.datastax.driver.core.PreparedStatement; -import com.datastax.driver.core.BoundStatement; -import compbio.cassandra.CassandraReaderOld; import compbio.cassandra.Pair; -import compbio.engine.ProteoCachePropertyHelperManager; -import compbio.util.PropertyHelper; public class CassandraReaderExecutionTime { private Session session; diff --git a/datadb/compbio/cassandra/readers/DailyStatisticsReader.java b/datadb/compbio/cassandra/readers/DailyStatisticsReader.java index 718a404..4646537 100644 --- a/datadb/compbio/cassandra/readers/DailyStatisticsReader.java +++ b/datadb/compbio/cassandra/readers/DailyStatisticsReader.java @@ -18,16 +18,17 @@ public class DailyStatisticsReader extends CassandraReader { public DailyStatisticsReader() { super(); } - + /** * query: total number of jobs for the period from date1 till date2 * * @param dateStart - * the first date in the period + * the first date in the period * @param dateEnd - * the last date in the period + * the last date in the period * - * @return TotalJobsStatisticBean to the controller DailyStatisticsController + * @return TotalJobsStatisticBean to the controller + * DailyStatisticsController **/ public TotalJobsStatisticBean query(long dateStart, long dateEnd) { Calendar start = Calendar.getInstance(); @@ -59,20 +60,20 @@ public class DailyStatisticsReader extends CassandraReader { query.setWholeTotal(wholeTotal); return query; } - + /** * query: jobs and sequence at a date * * @param day - * the date in long format + * the date in long format * @param date - * the date in String format + * the date in String format * * @param status - * final job status + * final job status * @return DateBean to the controller DailyStatisticsController **/ - public DateBean readJobByDay(long day, String date, JobStatus status) { + public DateBean readJobByDay(long day, String date, JobStatus status) { DateBean res = new DateBean(date); if (status == JobStatus.OK) { ResultSet results = CassandraQuery("SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";"); @@ -82,9 +83,9 @@ public class DailyStatisticsReader extends CassandraReader { for (Row r : rows) { res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein")); } - } - else { - ResultSet results = CassandraQuery("SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + "';"); + } else { + ResultSet results = CassandraQuery("SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + + "';"); if (results == null || results.isExhausted()) return null; List rows = results.all(); diff --git a/datadb/compbio/cassandra/readers/IpReader.java b/datadb/compbio/cassandra/readers/IpReader.java index 2928b70..43c2817 100644 --- a/datadb/compbio/cassandra/readers/IpReader.java +++ b/datadb/compbio/cassandra/readers/IpReader.java @@ -10,11 +10,11 @@ import com.datastax.driver.core.Row; import compbio.beans.UserBean; public class IpReader extends CassandraReader { - + public IpReader() { super(); } - + /** * query jobs by ip * @@ -31,7 +31,7 @@ public class IpReader extends CassandraReader { for (Row r : rows) { if (r.getString("FinalStatus").equals("OK")) { String date = r.getString("DataBegin"); - res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") }); + res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") }); } } UserBean query = new UserBean(ip); diff --git a/datadb/compbio/cassandra/readers/JobReader.java b/datadb/compbio/cassandra/readers/JobReader.java index 6d39b04..178ff4b 100644 --- a/datadb/compbio/cassandra/readers/JobReader.java +++ b/datadb/compbio/cassandra/readers/JobReader.java @@ -6,7 +6,7 @@ import com.datastax.driver.core.Row; import compbio.beans.JobBean; public class JobReader extends CassandraReader { - + public JobReader() { super(); } diff --git a/datadb/compbio/cassandra/readers/PredictionReader.java b/datadb/compbio/cassandra/readers/PredictionReader.java index b7613a3..73e7dbf 100644 --- a/datadb/compbio/cassandra/readers/PredictionReader.java +++ b/datadb/compbio/cassandra/readers/PredictionReader.java @@ -8,19 +8,19 @@ import com.datastax.driver.core.ResultSet; import com.datastax.driver.core.Row; public class PredictionReader extends CassandraReader { - + public PredictionReader() { super(); } - + /** * query: protein feature * - * @param feature - * a feature of secondary structure: Helix or Beta Sheet - * - * @param percent - * fraction the feature in the protein + * @param feature + * a feature of secondary structure: Helix or Beta Sheet + * + * @param percent + * fraction the feature in the protein * * @return Map to the controller SSFeaturesController * @@ -34,8 +34,8 @@ public class PredictionReader extends CassandraReader { for (Row r : rows) { String prot = r.getString("Protein"); String prediction = findJnetpred(r.getMap("Predictions", String.class, String.class)); - if (prot != null || prediction != null) { - if (prediction.replaceAll("[^"+feature+"]", "").length() > prediction.length() * percent / 100) { + if (prot != null || prediction != null) { + if (prediction.replaceAll("[^" + feature + "]", "").length() > prediction.length() * percent / 100) { query.put(prot, prediction); } } @@ -43,9 +43,9 @@ public class PredictionReader extends CassandraReader { return query; } - private String findJnetpred (Map pred) { + private String findJnetpred(Map pred) { if (pred != null) { - if (pred.containsKey("jnetpred")) + if (pred.containsKey("jnetpred")) return pred.get("jnetpred"); } return null; diff --git a/datadb/compbio/cassandra/readers/ProteoDAO.java b/datadb/compbio/cassandra/readers/ProteoDAO.java index 0b6f689..75755b6 100644 --- a/datadb/compbio/cassandra/readers/ProteoDAO.java +++ b/datadb/compbio/cassandra/readers/ProteoDAO.java @@ -1,10 +1,7 @@ package compbio.cassandra.readers; - public interface ProteoDAO { - + E query(long dateStart, long dateEnd); - - } diff --git a/datadb/compbio/cassandra/readers/ReaderByCounter.java b/datadb/compbio/cassandra/readers/ReaderByCounter.java index 9a2bd5e..184fd57 100644 --- a/datadb/compbio/cassandra/readers/ReaderByCounter.java +++ b/datadb/compbio/cassandra/readers/ReaderByCounter.java @@ -10,27 +10,25 @@ import com.datastax.driver.core.Row; import compbio.beans.TotalByCounterBean; -public class ReaderByCounter extends CassandraReader{ - +public class ReaderByCounter extends CassandraReader { + public ReaderByCounter() { super(); } - - - + /** * query protein sequences with number of jobs - * + * * @param minimalcounter * * @return List to the controller SequenceController * **/ - public List readProteinByCounter(int minimalcounter) { + public List readProteinByCounter(int minimalcounter) { ResultSet results = CassandraQuery("SELECT Protein, JobID FROM ProteinRow;"); return QueryByCounter(results, "Protein", minimalcounter); } - + /** * query ip with number of jobs * @@ -43,18 +41,17 @@ public class ReaderByCounter extends CassandraReader{ ResultSet results = CassandraQuery("SELECT JobID, ip FROM ProteinLog;"); return QueryByCounter(results, "ip", minimalcounter); } - - + /** * query number of jobs by counter and parameter: ip or protein * * @param results - * cassandra query result + * cassandra query result * @param counterParameter - * parameter for a query: ip or proteint + * parameter for a query: ip or proteint * @param minimalcounter - * - * @return List + * + * @return List * **/ public List QueryByCounter(ResultSet results, String counterParameter, int minimalcounter) { @@ -79,6 +76,6 @@ public class ReaderByCounter extends CassandraReader{ } } return query; - } - + } + } diff --git a/datadb/compbio/cassandra/readers/SequenceReader.java b/datadb/compbio/cassandra/readers/SequenceReader.java index 244902f..0aedbb2 100644 --- a/datadb/compbio/cassandra/readers/SequenceReader.java +++ b/datadb/compbio/cassandra/readers/SequenceReader.java @@ -13,14 +13,14 @@ public class SequenceReader extends CassandraReader { public SequenceReader() { super(); } - + /** * query: protein sequence - * + * * @param protIn - * protein sequence or partial of protein sequence + * protein sequence or partial of protein sequence * @param searchtype - * "whole" or "partial" of protein sequence + * "whole" or "partial" of protein sequence * * @return List to the controller SequenceController * @@ -58,16 +58,17 @@ public class SequenceReader extends CassandraReader { } return query; } - + /** - * create a list of parts of protein sequence for highlighting current value in report; - * + * create a list of parts of protein sequence for highlighting current value + * in report; + * * @param protein - * protein sequence + * protein sequence * @param subprot - * partial of protein sequence + * partial of protein sequence * - * @return List + * @return List * **/ private static List CreateSubprotein(String protein, String subprot) { diff --git a/engine/compbio/engine/Job.java b/engine/compbio/engine/Job.java index 309e0e9..e1de779 100644 --- a/engine/compbio/engine/Job.java +++ b/engine/compbio/engine/Job.java @@ -19,14 +19,14 @@ public class Job { private long StartingTime; private long ExecutionTime; - static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");; + static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");; static SimpleDateFormat timeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s"); public Job() { ExecutionStatus = "OK"; FinalStatus = "OK"; jobid = ""; - + StartingDateStr = "1970/1/1"; StartingTimeStr = "1970/1/1:0:0:0"; EndTimeStr = "1970/1/1:0:0:0"; @@ -43,7 +43,7 @@ public class Job { setDates(date1, date2); } - protected void setDates (String d1, String d2) { + protected void setDates(String d1, String d2) { StartingTimeStr = d1; StartingDateStr = d1.substring(0, d1.indexOf(":")); StartingTime = convertTime(StartingTimeStr); @@ -53,9 +53,8 @@ public class Job { EndTime = convertTime(d2); ExecutionTime = EndTime - StartingTime; } - - - protected long convertDate (String d) { + + protected long convertDate(String d) { try { if (null != d) { Date startdate = dateformatter.parse(d); @@ -66,8 +65,8 @@ public class Job { } return 0L; } - - protected long convertTime (String d) { + + protected long convertTime(String d) { try { if (null != d) { Date startdate = timeformatter.parse(d); @@ -78,8 +77,7 @@ public class Job { } return 0L; } - - + public void setStartingDate(String date) { this.StartingDateStr = date; StartingDate = convertDate(date); @@ -100,12 +98,15 @@ public class Job { public String getStartingDateStr() { return StartingDateStr; } + public String getStartingTimeStr() { return StartingTimeStr; } + public long getStartingDate() { return StartingDate; } + public long getStartingTime() { return StartingTime; } @@ -113,6 +114,7 @@ public class Job { public String getEndTimeStr() { return EndTimeStr; } + public long getEndTime() { return EndTime; } @@ -124,7 +126,7 @@ public class Job { public void setFinalStatus(String status) { FinalStatus = status; } - + public String getExecutionStatus() { return ExecutionStatus; } @@ -136,7 +138,7 @@ public class Job { public long getExecutionTime() { return ExecutionTime; } - + public void setIP(String IP) { this.IP = IP; } @@ -146,7 +148,7 @@ public class Job { return IP; return "127.0.0.1"; } - + public void setEmail(String email) { this.Email = email; } diff --git a/engine/compbio/engine/JpredJob.java b/engine/compbio/engine/JpredJob.java index db4a7fe..522ad9f 100644 --- a/engine/compbio/engine/JpredJob.java +++ b/engine/compbio/engine/JpredJob.java @@ -19,7 +19,7 @@ public class JpredJob extends Job { super(jobid, date1, date2); this.protein = protein; predictions = new ArrayList(); - alignment = new ArrayList(); + alignment = new ArrayList(); log = ""; } @@ -27,7 +27,7 @@ public class JpredJob extends Job { super(jobid, date1, date2); this.protein = protein; this.alignment = alignment; - this.predictions = predictions; + this.predictions = predictions; } public void setProtein(String protein) { diff --git a/engine/compbio/engine/ProteoCachePropertyHelperManager.java b/engine/compbio/engine/ProteoCachePropertyHelperManager.java index 4615297..f5f67bb 100644 --- a/engine/compbio/engine/ProteoCachePropertyHelperManager.java +++ b/engine/compbio/engine/ProteoCachePropertyHelperManager.java @@ -34,26 +34,22 @@ public final class ProteoCachePropertyHelperManager { private static PropertyHelper ph = null; /** - * Ways to fix path problem: - * 1) find a path to WEB-INF directory based on the path to a known class. - * Then prepend this absolute path to the rest of paths - * pros: no input from user - * cons: relocation of the source may cause problems + * Ways to fix path problem: 1) find a path to WEB-INF directory based on + * the path to a known class. Then prepend this absolute path to the rest of + * paths pros: no input from user cons: relocation of the source may cause + * problems * - * 2) Require users to add configuration directories to the class - * path and then load entries from it. - * pros: - * cons: Many paths needs to be added. Put significant burden on the user. - * Hard to tell web appl server to add these entries to its class path. + * 2) Require users to add configuration directories to the class path and + * then load entries from it. pros: cons: Many paths needs to be added. Put + * significant burden on the user. Hard to tell web appl server to add these + * entries to its class path. * - * 3) Ask for project source directory explicitly in the configuration. - * pros: - * cons: similar to 1, but this initial configuration file must reside in - * well known location! Why ask users what can be found automatically? + * 3) Ask for project source directory explicitly in the configuration. + * pros: cons: similar to 1, but this initial configuration file must reside + * in well known location! Why ask users what can be found automatically? * - * 4) Have everything in the location already in class path for tomcat. - * pros: - * cons: only classes and lib/*.jar are added, Eclipse will remove non + * 4) Have everything in the location already in class path for tomcat. + * pros: cons: only classes and lib/*.jar are added, Eclipse will remove non * classses from classes dir. * * Try 1 - succeed. @@ -84,11 +80,8 @@ public final class ProteoCachePropertyHelperManager { /** * Method return the absolute path to the project root directory. It assumes - * the following structure of the project: - * project-root: - * conf/settings - * binaries - * WEB-INF/classes/compbio/engine/conf/PropertyHelperManager.class + * the following structure of the project: project-root: conf/settings + * binaries WEB-INF/classes/compbio/engine/conf/PropertyHelperManager.class * If the structure changes it must be reflected in this method * * @return the local path @@ -112,8 +105,8 @@ public final class ProteoCachePropertyHelperManager { } catch (IllegalArgumentException e) { // Classes are in the jar file, using different method to determine // the path new File(INCORRECT URL) throws it - String mes = "It looks like classes are in the jar file. " - + "Attempting a different method to determinine the path to the resources"; + String mes = "It looks like classes are in the jar file. " + + "Attempting a different method to determinine the path to the resources"; log.debug(mes + e.getLocalizedMessage(), e.getCause()); try { f = new File(ProteoCachePropertyHelperManager.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath()); @@ -147,4 +140,5 @@ public final class ProteoCachePropertyHelperManager { return Boolean.parseBoolean(propValue); } return false; - }} + } +} diff --git a/engine/compbio/engine/archive/Archive.java b/engine/compbio/engine/archive/Archive.java index 392a737..8aad2aa 100644 --- a/engine/compbio/engine/archive/Archive.java +++ b/engine/compbio/engine/archive/Archive.java @@ -20,7 +20,7 @@ public class Archive { String path = ph.getProperty("archive.path"); assert (null != path); - if (isAbsolutePath (path)) { + if (isAbsolutePath(path)) { archivepath = path; } else { String abspath = ProteoCachePropertyHelperManager.getLocalPath(); @@ -31,20 +31,19 @@ public class Archive { } } - private boolean isAbsolutePath (String path) { - return (new File(path).isAbsolute()); + private boolean isAbsolutePath(String path) { + return (new File(path).isAbsolute()); } - - private boolean isDirExists (String path) throws IOException { + + private boolean isDirExists(String path) throws IOException { archive = new File(path); return archive.getCanonicalFile().isDirectory(); } - - public boolean addArchivedJob (ArchivedJob job) { + public boolean addArchivedJob(ArchivedJob job) { return true; } - + public String createJob(String jobid) { return archivepath + "/" + jobid + ".tar.gz"; } diff --git a/engine/compbio/engine/archive/ArchiveManager.java b/engine/compbio/engine/archive/ArchiveManager.java index dabaf3a..9b9979e 100644 --- a/engine/compbio/engine/archive/ArchiveManager.java +++ b/engine/compbio/engine/archive/ArchiveManager.java @@ -1,10 +1,8 @@ package compbio.engine.archive; -import java.io.File; import java.io.FileNotFoundException; -import java.io.InputStream; + import java.util.Iterator; -import java.util.Scanner; //import compbio.util.Util; @@ -17,11 +15,12 @@ import java.util.Scanner; */ public class ArchiveManager implements Iterator { Archive archive; - //private final Scanner input; + + // private final Scanner input; /** * Delimiter for the scanner */ - //private final String DELIM = ">"; + // private final String DELIM = ">"; /** * Header data can contain non-ASCII symbols and read in UTF8 @@ -36,25 +35,19 @@ public class ArchiveManager implements Iterator { */ public ArchiveManager(final String mainPath) throws FileNotFoundException { /* - input = new Scanner(new File(mainPath), "UTF8"); - input.useDelimiter(DELIM); - Runtime.getRuntime().addShutdownHook(new Thread() { - - @Override - public void run() { - if (input != null) { - input.close(); - } - } - }); - */ + * input = new Scanner(new File(mainPath), "UTF8"); + * input.useDelimiter(DELIM); Runtime.getRuntime().addShutdownHook(new + * Thread() { + * + * @Override public void run() { if (input != null) { input.close(); } } + * }); + */ } - + public ArchiveManager(Archive ar) { archive = ar; } - /** * {@inheritDoc} * @@ -63,7 +56,7 @@ public class ArchiveManager implements Iterator { */ @Override public boolean hasNext() { - //return input.hasNext(); + // return input.hasNext(); return true; } @@ -81,12 +74,10 @@ public class ArchiveManager implements Iterator { public ArchivedJob next() { String path = "bla-bla-bla"; /* - String path = input.next(); - while (fastaHeader.indexOf("\n") < 0 && input.hasNext()) { - path = fastaHeader.concat(">"); - path = fastaHeader.concat(input.next()); - } - */ + * String path = input.next(); while (fastaHeader.indexOf("\n") < 0 && + * input.hasNext()) { path = fastaHeader.concat(">"); path = + * fastaHeader.concat(input.next()); } + */ return new ArchivedJob(path); } @@ -105,7 +96,7 @@ public class ArchiveManager implements Iterator { * instance of the FastaReader will be possible after calling this method. */ public void close() { - //input.close(); + // input.close(); } private static ArchivedJob toFastaSequence(final String singleFastaEntry) { @@ -115,11 +106,9 @@ public class ArchiveManager implements Iterator { int nlineidx = singleFastaEntry.indexOf("\n"); if (nlineidx < 0) { - throw new AssertionError( - "The FASTA sequence must contain the header information" - + " separated by the new line from the sequence. Given sequence does not appear to " - + "contain the header! Given data:\n " - + singleFastaEntry); + throw new AssertionError("The FASTA sequence must contain the header information" + + " separated by the new line from the sequence. Given sequence does not appear to " + + "contain the header! Given data:\n " + singleFastaEntry); } String header = singleFastaEntry.substring(0, nlineidx); diff --git a/engine/compbio/engine/archive/ArchivedJob.java b/engine/compbio/engine/archive/ArchivedJob.java index 08ec64b..a07d77d 100644 --- a/engine/compbio/engine/archive/ArchivedJob.java +++ b/engine/compbio/engine/archive/ArchivedJob.java @@ -44,7 +44,7 @@ public class ArchivedJob { } if (Files.isReadable(Paths.get(thefile))) { Files.copy(Paths.get(thefile), Paths.get(finalpath)); - return resultpath + '/' + jobfilename; + return resultpath + '/' + jobfilename; } return null; } -- 1.7.10.2