diff --git a/act b/act
index 4200521ecdb9b2301b3e989c86fcdd295cd31de7..365fe5e99f0b2f974415a6a98724989ef8f45b62 100755
--- a/act
+++ b/act
@@ -43,6 +43,8 @@ CLASSPATH=$CLASSPATH:$ACT_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ACT_HOME/lib/iba
# picard jars
CLASSPATH=$ACT_HOME/lib/picard/sam.jar:$ACT_HOME/lib/picard/picard.jar:$CLASSPATH
+CLASSPATH="$ACT_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
+
export CLASSPATH
ACT_PROPERTIES="-Dartemis.environment=UNIX"
diff --git a/art b/art
index 180d77379adb6537595fc1b98b8891c9afaf550f..f8fe4fe68b42da14fac53d7ca48735e3b515c3e8 100755
--- a/art
+++ b/art
@@ -40,6 +40,9 @@ export CLASSPATH
# picard jars
CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ARTEMIS_HOME/lib/commons-net-2.2.jar:$CLASSPATH
+
+CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
+
export CLASSPATH
diff --git a/docs/act_start_chapter.sgml b/docs/act_start_chapter.sgml
index 45b24c13b8ad37e822055e3a4457b414f0d478e7..b41b4567748968b6a5f491584fc4dbb52cd947a6 100644
--- a/docs/act_start_chapter.sgml
+++ b/docs/act_start_chapter.sgml
@@ -170,7 +170,7 @@ cd ~/act
<PARA>
<COMMAND>
-java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain
+java -mx500m -ms100m -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/ibatis/cglib-nodep-2.2.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:lib/commons-lang-2.6.jar:lib/commons-net-2.2.jar:. uk.ac.sanger.artemis.components.ActMain
</COMMAND>
</PARA>
</SECT1>
diff --git a/docs/feature_edit.gif b/docs/feature_edit.gif
index a31014b869c0dca960a92b334975f26e20d8150e..3b46dab3f8cee1fb69021d2fcd67db89b15111f1 100644
Binary files a/docs/feature_edit.gif and b/docs/feature_edit.gif differ
diff --git a/docs/jvm_options.sgml b/docs/jvm_options.sgml
index 242ae1fa2f603265a42a7b498a302a41971451e6..65dde42851e085b37b58c39e49611f2aed027e1e 100644
--- a/docs/jvm_options.sgml
+++ b/docs/jvm_options.sgml
@@ -99,6 +99,29 @@ first (top) sequence in ACT:
</SECT2>
]]>
+ <SECT2 ID="JVM-SHOW-SNPS">
+ <TITLE><LITERAL>-Dshow_snps</LITERAL></TITLE>
+ <PARA>
+Show SNP marks in BAM panels.
+</PARA>
+ </SECT2>
+
+ <SECT2 ID="JVM-SHOW-SNPS-PLOT">
+ <TITLE><LITERAL>-Dshow_snp_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open SNP plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
+ <SECT2 ID="JVM-SHOW-COV-PLOT">
+ <TITLE><LITERAL>-Dshow_cov_plot</LITERAL></TITLE>
+ <PARA>
+Automatically open coverage plots for BAM files that are opened.
+</PARA>
+ </SECT2>
+
+
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
diff --git a/docs/main_window_chapter.sgml b/docs/main_window_chapter.sgml
index b670839d26bd333cc2b22531f80893508648eb73..7dc2bee94c0f6a3e6051ded94b8bd94adb913a9a 100644
--- a/docs/main_window_chapter.sgml
+++ b/docs/main_window_chapter.sgml
@@ -265,5 +265,6 @@ menu items which allow the maximum window size to be set.
</PARA>
</SECT1>
+&validator;
&mousebuttons;
</CHAPTER>
diff --git a/docs/manual.sgml b/docs/manual.sgml
index 3ce768f8da3f08f5338fd7c529f4472424cad863..1e1f57c36eab1ab7411075678b05e32603bc178c 100644
--- a/docs/manual.sgml
+++ b/docs/manual.sgml
@@ -21,6 +21,7 @@
<!ENTITY views-directedit SYSTEM "views_directedit.sgml">
<!ENTITY featurelist SYSTEM "feature_list.sgml">
<!ENTITY mousebuttons SYSTEM "mousebuttons.sgml">
+<!ENTITY validator SYSTEM "validator.sgml">
<!ENTITY gettingjava SYSTEM "getting_java.sgml">
<!ENTITY unixargs SYSTEM "unix_args.sgml">
<!ENTITY jvmopts SYSTEM "jvm_options.sgml">
diff --git a/docs/menus.sgml b/docs/menus.sgml
index 204540fcbd4f2821e8f46a883a6a2f08d4218af6..21782ecc2aa694c3c39b51bd72b9be641784a1b9 100644
--- a/docs/menus.sgml
+++ b/docs/menus.sgml
@@ -165,11 +165,22 @@ similar effect to double clicking the middle button on a base or residue (see
<TITLE>Features Overlapping Selection</TITLE>
<PARA>
Select those (and only those) features that overlap the currently selected
-range of bases or any of the currently selected features. The current
+range of bases or any of the currently selected features. The current
selection will be discarded.
</PARA>
</SECT2>
+
+ <SECT2 ID="SELECTMENU-WITHIN-SELECTION">
+ <TITLE>Features Within Selection</TITLE>
+ <PARA>
+Select those (and only those) features that are fully contained by the currently
+selected range of bases or any of the currently selected features. The current
+selection will be discarded.
+ </PARA>
+ </SECT2>
+
+
<SECT2 ID="SELECTMENU-BASE-RANGE">
<TITLE>Base Range ...</TITLE>
<PARA>
@@ -535,6 +546,16 @@ LINKEND="GRAPHS">. Configuration options for graphs are described in <XREF
LINKEND="OPTIONS-PLOTS">.
</PARA>
</SECT2>
+
+<![ %act-only; [
+ <SECT2 ID="VIEWMENU-ADJUST-HEIGHTS">
+ <TITLE>Adjust panel heights ...</TITLE>
+ <PARA>
+Option in ACT for adjusting the panel heights (BAM, VCF, plots, comparisons) by giving
+them different weights in order to distribute the space between each component.
+ </PARA>
+ </SECT2>
+]]>
</SECT1>
<SECT1 ID="GOTOMENU">
@@ -775,9 +796,6 @@ The feature edit window
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="feature_edit.gif">
</IMAGEOBJECT>
- <IMAGEOBJECT>
- <IMAGEDATA FORMAT="eps" FILEREF="feature_edit.eps">
- </IMAGEOBJECT>
</MEDIAOBJECT>
</SCREENSHOT>
<PARA>
@@ -839,9 +857,35 @@ LINKEND="GOTOMENU-GOTO-SELECTION-START"> for more).
</LISTITEM>
<LISTITEM>
<PARA>
-The <LITERAL>Select Feature</LITERAL> button selects this feature (in the same
-way as clicking on the feature in one of the views).
+The <LITERAL>User Qualifiers</LITERAL> button opens a tool for maintaining
+user defined lists of qualifiers (i.e. qualifiers in the form tag = value pairs
+on separate lines) and the option to read qualifiers from <ULINK
+URL="http://www.geneontology.org/GO.format.shtml" TYPE="external">OBO</ULINK> formatted files or
+URLs. In the intial screen (see below) you are invited to import your qualifier list from the import
+options in the "File" menu. These lists can be optionally saved between sessions in the file
+'.artemis.qualifiers' in the home directory.
</PARA>
+ <MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="gif" FILEREF="qualifier_list.gif">
+ </IMAGEOBJECT>
+ </MEDIAOBJECT>
+
+ <PARA>
+When a qualifier list or OBO file has been added then it is possible to search for
+keywords within a list. The qualifer selected in the drop down list (under the SEARCH button)
+can then be added to the current feature annotation or added to selected features in &prog;.
+If the keywords text field is left blank then all qualifiers are available from the drop
+down list of qualifier values.
+ </PARA>
+
+ <MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="gif" FILEREF="qualifier_list2.gif">
+ </IMAGEOBJECT>
+ </MEDIAOBJECT>
+
+
</LISTITEM>
</ITEMIZEDLIST>
</LISTITEM>
diff --git a/docs/qualifier_list.gif b/docs/qualifier_list.gif
new file mode 100644
index 0000000000000000000000000000000000000000..3bcd2f0cdbd99bfa2d21e14cf856e0f2bdbab25a
Binary files /dev/null and b/docs/qualifier_list.gif differ
diff --git a/docs/qualifier_list2.gif b/docs/qualifier_list2.gif
new file mode 100644
index 0000000000000000000000000000000000000000..c963b159ac03f87ace73f7ebd642eadb6a0ac6d7
Binary files /dev/null and b/docs/qualifier_list2.gif differ
diff --git a/docs/start_chapter.sgml b/docs/start_chapter.sgml
index 42d645dc0a25cc2a072f1bc1a47f35b2768890be..ffb0367fac1c85cad18812aa76dd903796a656d8 100644
--- a/docs/start_chapter.sgml
+++ b/docs/start_chapter.sgml
@@ -66,7 +66,7 @@ cd ~/artemis
<PARA>
<COMMAND>
-java -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/chado-14-interface.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain
+java -mx500m -ms100m -classpath lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/ibatis/cglib-nodep-2.2.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard.jar:lib/picard/sam.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-codec.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:lib/commons-lang-2.6.jar:lib/commons-net-2.2.jar:. -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ArtemisMain
</COMMAND>
</PARA>
</SECT1>
diff --git a/docs/tick.png b/docs/tick.png
new file mode 100644
index 0000000000000000000000000000000000000000..9bf53b96bef1b0c7db034241a70e0f8db1a0173a
Binary files /dev/null and b/docs/tick.png differ
diff --git a/docs/unix_args.sgml b/docs/unix_args.sgml
index 4b996dfa4ee599cf91a36ca1d0c99fe928fea9b2..68c37c2019050a73c87bdd3a3e9a2d1154f98ed7 100644
--- a/docs/unix_args.sgml
+++ b/docs/unix_args.sgml
@@ -5,14 +5,6 @@ As well as the listing file names on the command line, the following switches
are available to UNIX users:
</PARA>
- <SECT2 ID="UNIXARGS-QUIET">
- <TITLE><LITERAL>-quiet</LITERAL></TITLE>
- <PARA>
-This option tells &prog; to suppress normal informational messages while
-running.
- </PARA>
- </SECT2>
-
<SECT2 ID="UNIXARGS-OPTIONS">
<TITLE><LITERAL>-options</LITERAL></TITLE>
<PARA>
diff --git a/docs/validation_report.png b/docs/validation_report.png
new file mode 100644
index 0000000000000000000000000000000000000000..ab379078da4a6655f30d90ee1d73a5a1435fd1c8
Binary files /dev/null and b/docs/validation_report.png differ
diff --git a/docs/validator.sgml b/docs/validator.sgml
new file mode 100644
index 0000000000000000000000000000000000000000..f2a8ff120c3a0b2cfbe4cd6c55c60e93b19e0461
--- /dev/null
+++ b/docs/validator.sgml
@@ -0,0 +1,181 @@
+ <SECT1 ID="VALIDATOR">
+ <TITLE>Annotation Validation</TITLE>
+
+<SECT2 ID="VALIDATOR-RUN">
+ <TITLE>How to Run Validation Checks</TITLE>
+ <PARA>
+&prog; can carry out validations checks to try and minimise annotation errors.
+These checks can be carried out in the following ways:
+ </PARA>
+<ORDEREDLIST ID="VALID-CHECK">
+ <LISTITEM ID="VALID-CHECK-1">
+ <PARA>
+Click on the tick button
+
+<inlinemediaobject>
+ <imageobject>
+ <imagedata fileref="tick.png">
+ </imageobject>
+</inlinemediaobject>
+
+found in the top right hand side of Artemis to validate all features. When complete it will
+open a report window highlighting any features which have failed the checks.
+
+ </PARA>
+ </LISTITEM>
+ <LISTITEM ID="VALID-CHECK-2">
+ <PARA>
+Select the features to be checked in &prog; and open the popup menu by right clicking on the feature display
+and selecting the 'Validation report ...' option.
+ </PARA>
+ </LISTITEM>
+
+ <LISTITEM ID="VALID-CHECK-3">
+ <PARA>
+From the View menu, select the 'Feature Filters' menu item and the 'Validation checks...' option. This opens
+a feature list window for each of the type of check it carries out and these contain the features that have
+failed the check.
+ </PARA>
+ </LISTITEM>
+ <LISTITEM ID="VALID-CHECK-4">
+ <PARA>
+For organisms in a chado database the vaidator can be run from the 'Database and File Manager' window from the
+'File' menu by selecting the 'Validate Selected Sequence / Organism' option.
+ </PARA>
+ </LISTITEM>
+</ORDEREDLIST>
+</SECT2>
+
+<SECT2 ID="VALIDATOR-CHECKS-ALL">
+ <TITLE>Validation Checks For All File Types</TITLE>
+ <PARA>
+The following checks are made on all file types (e.g. EMBL, GFF3):
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+CDS have no internal stop codon
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+CDS have a valid stop codon
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+
+ <PARA>
+Additionally &prog; checks GO annotation for:
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+unexpected white space in with/from and dbxref columns
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+the WITH/FROM field must be empty when using IDA, NAS, ND, TAS or EXP evidence code
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+GO:0005515 can only have IPI evidence code
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+IEP is not allowed for molecular_function and cellular_component terms
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+the WITH/FROM field must be filled when using ISS, ISA, ISO and ISM codes
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+</SECT2>
+
+<SECT2 ID="VALIDATOR-CHECKS-GFF">
+ <TITLE>Validation Checks For GFF3</TITLE>
+
+ <PARA>
+The following are checks for GFF3 and Chado entries only:
+ </PARA>
+
+<ITEMIZEDLIST SPACING="compact">
+ <LISTITEM>
+ <PARA>
+check that the gene model comprises of at least a gene and a transcript feature
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that the boundaries of the features making up a gene model are consistent
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that all the features in a gene model are on the same strand
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that CDS features have a phase
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check the attribute column to ensure that qualifiers have a value (not empty) and
+that only reserved tags start with an uppercase character
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that partial qualifiers are consistent within a gene model
+ </PARA>
+ </LISTITEM>
+ <LISTITEM>
+ <PARA>
+check that the gene name prefix is consistent within a gene model
+ </PARA>
+ </LISTITEM>
+</ITEMIZEDLIST>
+
+</SECT2>
+
+<SECT2 ID="VALIDATOR-REPORT">
+ <TITLE>Validation Report</TITLE>
+
+ <PARA>
+The validation report window displays a summary for the features that have failed one or
+more of the annotation checks above. The title bar of the window displays the number of
+features that have passed and the number that have failed the validation checks. The
+problems identified are highlighted in red.
+ </PARA>
+
+ <PARA>
+<MEDIAOBJECT>
+ <IMAGEOBJECT>
+ <IMAGEDATA FORMAT="png" FILEREF="validation_report.png"></IMAGEOBJECT>
+ </MEDIAOBJECT>
+ </PARA>
+
+ <PARA>
+Some of the errors can be fixed automatically. The 'Auto-Fix' button opens a window
+with the fixes enabled that are available for the entry type that is loaded in &prog;. For example, it will
+attempt to fix CDS features that have been found not to end in stop codons. If the last codon is not a
+stop codon, but the very next codon is a stop codon, then the end of the feature is
+extended by three bases.
+ </PARA>
+ <PARA>
+For GFF3 and chado entries &prog; will also attempt to fix problems it finds with gene
+boundaries and if a phase is absent then a default phase of 0 is given. Once these are
+fixed the results window will automatically update and remove the problems it has
+managed to resolved.
+ </PARA>
+</SECT2>
+
+ </SECT1>
diff --git a/etc/writedb_entry b/etc/writedb_entry
index 12e7f55bd481f34ce6093299e205d19c2daf9f82..6fbfcb6cb4055a4dee589bd19b21543277babe45 100755
--- a/etc/writedb_entry
+++ b/etc/writedb_entry
@@ -28,7 +28,7 @@ done
ARTEMIS_HOME=`dirname "$PRG"`/..
CLASSPATH="$ARTEMIS_HOME:$ARTEMIS_HOME/lib/biojava.jar:$ARTEMIS_HOME/lib/jemAlign.jar:$ARTEMIS_HOME/lib/jakarta-regexp-1.2.jar:$ARTEMIS_HOME/lib/macos.jar:$ARTEMIS_HOME/lib/postgresql-8.4-701.jdbc3.jar:$ARTEMIS_HOME/lib/chado-14-interface.jar:$CLASSPATH"
-CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/commons-lang-2.6.jar"
+CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH"
# iBatis jars
CLASSPATH="$CLASSPATH:$ARTEMIS_HOME/lib/ibatis/ibatis-2.3.4.726.jar:$ARTEMIS_HOME/lib/ibatis/:$ARTEMIS_HOME/lib/ibatis/log4j-1.2.14.jar:$ARTEMIS_HOME/lib/ibatis/cglib-nodep-2.2.jar:$ARTEMIS_HOME/lib/retrotranslator-runtime-1.1.0.jar"
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index bfec1da894ca1d501f6e59cf8c971b9984bae9ac..f4a0a9b441cf0644448028f0295b274584b14f50 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -892,12 +892,29 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
}
};
+ GFF3AttributeAggregator curcomProc = new GFF3AttributeAggregator() {
+ @Override
+ public String process(StringVector values) {
+ StringBuilder buffer = new StringBuilder();
+ if (values != null && values.size() > 0) {
+ for (int value_index = 0; value_index < values.size(); ++value_index) {
+ buffer.append(GFF3Encoder.encode(values.elementAt(value_index)));
+ if (value_index < (values.size()) - 1)
+ buffer.append(" ");
+ }
+ }
+ return buffer.toString();
+ }
+ };
+
// map GO -> full_GO
abuf.setMapping("GO", "full_GO");
abuf.setGlue("full_GO", ",");
// merge curation and comment
abuf.setMapping("curation", "comment");
+ abuf.setGlue("comment", " ");
+ abuf.setAggregator("comment", curcomProc);
// also put GOs in Ontology_term
abuf.setClone("full_GO", "Ontology_term");
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 6addbd4fa2b71679539867aabd4e32301bc0f5a2..f96025548a42d33a4f8cf268088ec0fe0bccb1dc 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -67,10 +67,12 @@ import org.postgresql.largeobject.LargeObjectManager;
import com.ibatis.common.jdbc.SimpleDataSource;
import java.sql.*;
+import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.io.*;
import java.net.ConnectException;
import java.net.InetAddress;
+import java.util.Calendar;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
@@ -551,7 +553,11 @@ public class DatabaseDocument extends Document
ByteBuffer entryBuffer = new ByteBuffer();
try
{
+ DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
+ Calendar cal = Calendar.getInstance();
+
entryBuffer.append("##gff-version 3\n");
+ entryBuffer.append("#created " + dateFormat.format(cal.getTime()) + "\n");
ByteBuffer sequenceBuffer = new ByteBuffer();
if(dao instanceof IBatisDAO)